It's not written anywhere rules-wise, this is a completely grey area how it would affect shapechanging, but using a bit of common sense it should be fairly obvious why prothetics limbs and cybernetic implants would interfere with shapechanging. There is nothing that suggests that it shouldn't be more difficult, to the contrary there is when you look at the lore. First of all, it's important to establish that all cybernetic implants mainly either falls into the category of being a replacement or an enhancement, furthermore it's equally important to acknowledge that a cybernetic implant is an artificial biomechanical device that is connected with wires and other things with the body.
Replacements: Replacements were prosthetic or artificial units intended to replace lost limbs and damaged organs. Common replacements provided no benefits other than duplicating the essential functions of their biological counterparts, and they presented little strain on the beneficiary's overall well-being. In appearance, a cybernetic replacement could be recognizably artificial or virtually indistinguishable from the real thing.

Enhancements: Enhancements bestowed new abilities or improved the recipient in some fashion. Enhancements included skeletal reinforcement, subcutaneous communications hardware, and weapon mounts. Some enhancements had visible external components, while others were hidden beneath the skin. Enhancements put more of a drain on the body's resources, and recipients frequently suffered debilitating physical or mental side effects.
You say that I want shapechanging to suffer penalties to any skill check when trying to trick others, which is quite far from correct - I want only the shapechanging action to be affected when the shapechanger in question has cybernetic implants and tries to shapechange - What else the character does to try do when attempting to trick others, which isn't shapechanging is irrelevant, like why they shapechange is irrelevant.
For those willing to make the sacrifice of flesh and expense, the body could be "upgraded" to allow for additional skills and abilities. Some involved modifying the limbs and internal systems of the potential patient. As with everything in the galaxy, this came at a potential price, in credits and in the potential loss of self. 
However, I did not declare it as fact that having prostethics/cybernetics interferes with shapechanging in the way you said I said it interferes - I declared as fact that "it impacts the narrative positively even if it impacts the character negatively, because this will reflect narratively cybernetics implants and prothetics interferes with shapechanging".
What I'm suggesting doesn't have anything to do with bothersome minute tracking. It's completely reasonable that it complicates the shapechanging process and there is a serious risk in attempting to shapechange with cybernetic implants or prostethic limbs, as the character has no control over how and what it's connected to in the body.
What you quoted there wasn't specifically aimed at you, but was meant in general. What was meant with that, is that just because something bad happens in the game, doesn't mean it's bad for the narrative and the game. It's an ongoing story being told, and while players won't always like what happens with their characters, but that doesn't mean that it can't be fun and entertaining.
Just because you don't see the narrative benefit, doesn't mean there isn't one.
One of the narrative benefits I see this mechanic have, is that it narratively can reflect cybernetic implants and prostethic limbs, replacements and enhancements, sometimes can interfere with shapechanging, but also how a shapechanger with sufficient insights about cybernetics could stop it from interfering.

Prothetic limbs adds both cosmetics and function, just not any new functions. However cybernetic implants on the other hand, does very much so add NEW functions and thus new benefits.
Furthermore, this would only be relevant for shapechangers. It would only cause them damage IF they trigger it, not straight up damage just from shapechanging while having cybernetic implants or prosthetics installed.
You seem to forget that shapechangers already have a benefit that most don't have - the ability to shapechange, installing cybernetic implants and prothetics should come at a sacrifice in relation to shapechanging.
Just because something can impact a character negatively, doesn't mean it's a negative narrative impact, in fact I'd say it impacts the narrative positively even if it impacts the character negatively, because this will reflect narratively cybernetics implants and prothetics interferes with shapechanging - it's not all just a bunch of numbers and stuff, it all carries a meaning. In my opinion, it would enrich the gaming experience, but then again some people only view the bad stuff that happens in game, as only bad.

That may be so that they are more advanced, but they're still BEYOND the shapeshifters control, they don't have in regards to shapechanging any control over the prosthetic limb or any other cybernetic implant for that matter.
Whether or not someone who's had a prostethic limb or cybernetics implant for a long time thinks it's just a part of them, doesn't change the fact that biologically they're artificial, not normally part of them. I don't want to incur penalty dice for the prosthetic limbs or cybernetic implants intended function - ONLY with regards to shapechanging because they don't have any control over how the prostethic limbs or cybernetic implants are CONNECTED to their body internally, and because of this the check should be more difficult, and obviously the more they have connectred the more difficult it would be to shapechange WITHOUT it resulting in it detrimentally impacting the character.

Btw this is the mitsurugi 3k to illustrate the if Darth Vader was a space samurai aesthetic, but the thing is super well balanced for 1 and 2 handed dueling, it just feels right in the hands and is small enough to hang on your belt (unlike the 2 handed legionnaire)
If I get super into lightsaber duelling I might buy one as a beater, with suncrusher blue in hilt led and a photon blade. Plecterpixel blades like what I got in the rev-n and mace are rated for medium dueling rather than heavy dueling.  In hilt led's are needed for heavy dueling and a photon blade with suncrusher blue led (3 blue led die's) will get you a superbright green blade https://vadersvault.com/photon-blade/ reportedly not quite as bright as plecterpixel but the next  brightest thing.

Vader's vault is 19 minutes from my dad's home in Cummings GA.  When I visited him in December I stopped by Vader's vault.  They had a limited run of mace windu replica lightsabers hilt by 89 sabers... and my son is Samuel L. so I bought one on the spot for his 5th birthday present, he'll be 2 this july...  it one of those "your father wanted you to have this when you were old enough" things.  And I ordered the pictured one for me so we could duel.  It's a rev-n elite with some custom machining and the pommel from the havoc to make it closer to the dimensions of a mitsurugi 3k which felt perfect in my hands but the whole "if Darth Vader was a space samurai this would be his lightsaber" aesthetic of the mitsurugi 3k just didn't do it for me.

So a thought (might be good, might be bad)...
Since you seem to be angling the route of Genesys with how it treats magic, why not have a single skill, such as Force Usage, or maybe even Force?  It'd be considered a default career skill for the F&D careers, but not for any of the specializations.  Not sure what characteristic to tie it to though; Saga Edition used Charisma, which would be Presence here, though Willpower seems to be the "default" if you consider Discipline to the be go-to skill for Force usage.
However, the catch is that in order to use a Force power, you still have to purchase the "base" power.  So in order to use Move, Enhance, and Sense, you'd have to shell out 30XP (10 XP per power).  Base difficulty is 1 purple to "activate" the power.
You don't have to purchase upgrades, but triggering them is an increase of difficulty per upgrade used where a Force Point is required, and then spend 2A to trigger that upgrade multiple times.
So for Move, to hurl a Silhouette 2 object that's at Medium Range, you'd be rolling Force skill against 3 purples (1 for base, +1 for Strength upgrade, +1 for Range upgrade) and would need to have 2A for the increase on the Strength upgrade.
For "Commit FD" effects, the PC instead downgrades their Force skill for each committed effect; so having Sense's defense Control upgrade active would change PC's Force skill dice pool built upon 3 characteristic and 2 skill ranks to be 1Y2G instead of the normal 2Y1G they'd otherwise be rolling.
Overall, I think changing it to a purely skill based system and not really using Force Rating is going to wind up making Force users a good deal more powerful, since they probably won't have to spread their XP nearly as far as they do currently, which in turn is one of the balancing factors FFG seems to have employed to keep Force users from ruling the roost as much as they had in prior RPGs.

@InfinityIncarnate have you looked at the Genesys game ffg has released that’s based on the same dice mechanic? It has an excellent magic system that you may find adapts in a far cleaner way to your concept.
The basics of it are:
Force Rating would become a 7th Characteristic
Add a set of 3 new Force Skills; Control, Sense, Alter
To use a force power you build a dice pool based on the Skill for the power and your Force Characteristic in the same way any other skill check is made.
Any talent that would allow a “combined force power check” instead allows you to substitute your Skill rank in a Force Skill for the usual skill, and to use the rules later on for adding success to a check.
Committing Force Rating simply reduces your Force Characteristic to temporarily increase another one if your six characteristics.
Each Force Power has a difficulty assigned to the base power and specific upgrades, this is how the base difficulty is determined for using a force power, eg:
Move, (Alter skill):
Basic: Easy Difficulty, 
Range: +1 Difficultly (1 Advantage to activate multiple times), 
Strength: +2 Difficultly to Increase Silhouette up to ranks in Strength purchased. 
Magnitude: +1 Difficulty to increase targets up to ranks in Magnitude (2 Advantage per additional activation), 
Control Hurl Attack becomes a Combat Check with all the usual modifiers, 
Other Control upgrades the same
 
Then to bring Morality into it you add something like the following rules:
Dark Side Force User:
For every uncancelled Success on a Force Skill Check the character gains 1 Conflict. After the roll but before spending Success or Advantage you may flip a Destiny Point and suffer Strain up to your Force Characteristic. You may choose to add an equal number of success to the results, or reduce conflict by an amount equal to the strain suffered (you may choose to do a combination of both).
 
Light Side Force User: 
After rolling a Force Skill Check a character may choose to flip a Destiny Point and suffer a number of Strain up to their Force Characteristic. Add a number of Success to the check equal to Strain suffered, the Force user also gains Conflict equal to the amount of Strain suffered.

And I'm saying your examples aren't proof of anything.
The variable nature of the system and the narrative nature of those scenes only say that, under one interpretation of them, would he require an FR higher than 2. 
And why not use a black pip? Again it's all about GM interpretation. How bad is the use of a black pip? Is it worth a tongue lashing? A slap on the wrist? Simple counseling? Nothing unless he makes a habit of it?
And Reliability is equally vague. You can't lock down what rolls are required for certain. You can't lock down difficulties. Or how well the player rolled, or what the GM interpreted as happening as a result.
One of the good (and bad) things about a tabletop game and the rules of this system is there isn't much by way of absolutes. You can do a lot with a little, or a little with a lot. It's all up to the GM and groups about what they find fun.
 
You might as well make the argument that the sky is orange...
It's not...
Except when it is.

Ok so to answer your specific question to me @infiniteincarnate I would not do anything to adjust force point generation as I find combined skill checks + the conflict/ strain/ destiny point usage enough to allow me to do things given specific situations. For example the situation you gave based on them being afraid I can simply have the player make a combined force power and discipline or cool check every time they want to use a force power, if they do not succeed at the cool/ discipline check it doesnt matter how many force points they generate they fail to use the force as they fail to concentrate.... this allows me to add setbacks and the like without any added complexity or difficulty. So ultimately I do not feel the need to change how FP are generated because it doesn't actually do anything to help or hinder the stories or the mechanics of the game for me, but again I will never tell people what to do at their table if they want to use house rules, this is just not want that solves a problem I am having, nor is it making something simpler and easier for me to run. Happy gaming everyone :).

Edit: I am not sure exactly how  your system works it was a bit complicated for me to understand so sorry about that and if this part doesnt actually make sense with your system, but if the person can choose if they generate light or dark, I feel that is to easy to stay light, that is also why i like the die as it is right now because the dark side is tempting to my players. Of course if this is not how it works then I am simply misunderstanding a couple of the arguments and never mind this spot :).

Edit 2: Luke lifting the X-wing would likely be a combination of pips and discipline check, either one failing or not generating enough would prevent the lifting of the x-wing. Good chance of failure, but this is also a big story moment anyway. Setbacks added for self doubt destiny point flipped against Disc roll. Luke FR likely 3 at this point actually.

Edit 3: I do think you should make sure your players understand this system, get a chance to try it out and then give them an opportunity to choose whether they want this one or the normal one. This game is about having fun so what ever makes it more fun is the way you should do it. Dont be discouraged one way or another. :).

Going to respond to just a couple things. The "not in stressful situation" thing you mentioned is why I like the house rule made by the person who made the stats thread (sorry cant remember your name please dont hate me, I know it starts with an A). where she allows a person to "take a 10" where they can always generate 2/3 of their FR in FP rounded up for what ever task without having to roll. This means they also generate what ever side they want. Mostly because during "non-stressful" situations you usually are not strapped for time so you could in theory just reroll the die as many times as you want till you get exactly what you need. This just makes it faster and doesnt have someone fishing for one of those .15% chance things with infinite retrys. 

As far as Luke's FR I know he is FR 3 because we actually have a stat block for Battle of Hoth Luke in the allies and adversaries book and he is FR 3. This is no surprise as Vader is FR 6 and we are talking big time main characters here. Luke and Vader are innately 2 of the most powerful force users in star wars history, even if Luke doesn't quite have the mastery, the force is ridiculously strong with him. 

Edit: Fear does lead to the dark side, but that doesnt mean the force works differently, it just leads the character to the dark side which is why failed fear checks generate conflict which can bring you closer to the dark. I understand where you are coming from, but I feel that the required use of skills and combined checks makes it moot in most of my games as a failed discipline check or a failed coordination check can be described as them being unable to feel the force properly regardless of what the force die rolls. I get why you want to change it, more power to you, but I can get most of what you are describing narratively with combined checks. It may just be because I do not take the force die as a narrative die, simply a mechanical thing that works alongside the narrative stuff and just allows me to randomly tempt my players with the dark side.

Edit: I may respond later with more but I will say if you are looking for a different system I do think you should check out the Genesys system for magic, BUT also make sure that when you do so you do not copy the way they do magic exactly. tweaking the magic rules and which "force skills" to match the types of force powers you allow in your game can be huge. In addition to this you would probably have to tweak how some of the talents work or just use genesys in general for your talent system. For dark side vs light I would probably use disadvantages and despairs to change some of the successes into dark... in addition to their normal effects, probably not all of their effects since some of the way genesys magic system works is by making magic a little "RNG", but ya look at "upgrades" maybe as things that can alter the difficulty or the like. Ultimately it may just give you some ideas on how to tweak your system to improve upon it.

For consideration of force power skills, Sense, Enhance, Mental, Attack, Defense. Just to name broad ones that aren't to broad. I think each of these skills could also be linked to a different characteristic rather than having ALL of them linked to will power, but that would be up to you.


(sense powers would be things like sense, seek and foresee) Enhance would be enhance and MAYBE Heal/harm. Mental would be influence/ misdirect, attack would be push, pull, lightning, bind. Defense would be protect, maybe heal. I guess we would need something for other versions of move so we could just use alter, for effects that do not end up here (moving things, force storms, so on and so forth).

I do hope this helps, obviously I am not trying to attack you or your system you are just trying to enjoy the game and want something that feels better for your system, as usual I like this the way it is so I won't use it, but if you are looking for ideas I hope this helps a little, since I know I am not smart enough to really come up with full on systems for you.

@tunewalker - I tried to respond to posts in a chronological order, I hope it doesn't cause any confusion.
The short answer is both yes and no, they can choose and no, because..:
The thing is, they can choose what to manifest, but it's the job of the circumstancial dice to affect the outcome in negative way, and for the most part there will be circumstancial dice, and even if there aren't, the GM can easily adjust it so that there are, because there will for the most part always be something in the situation that affects. Basically the circumstancial dice can cause:
- Strain and/or conflict in the user.
- Intended force points to change to the OPPOSITE of the intended.
- The check to fail altogether, with potentially additional consequences for such.

So what happens when there are no circumstancial dice? The force user can both partially succeed or completely succeed, but can also completely fail but with no additional consequences. But thing is, why is it that when a force user has the best conditions to use the force, that it should still be as difficult or easy as for instance when they have bad situations to deal with - because that is what the force dice always enforced - the same probabilities. It basically says that a force user always will have the same conditions no matter what. So for instance if you have light sided force user who's calm and at peace, in a serene and tranquil environment, but because of the static distribution of the sided forced points, it will be just difficult or easy as always. To me that doesn't make any kind of sense, a light sided force user would have even better odds at generating light sided points in such a situation. My system reflects that, but the force dice does not. It's also one of the reason's I wanted to make a system that isn't based on something static, and I wanted to use the inbuilt dice pool system as it would make the most sense to use as it would easily be able to integrate seamlessly with types of checks, and it would even open up to a variety of new things. Like for instance using the force during an offensive or defensive action, like a lightsaber attack - which we happen to see in the movies and shows.
I concur, however his force rating is 2 at best at this point - 2 is either a self-taught exile or a padawan, heck he might even just be a force rating 1 and the scene being an extended opposed check and him being lucky on his initial rolls, but later don't get the light side force points keep up the strength upgrade, which makes him give up.

My system would just use his current willpower, discipline and force rating and add relevant circumstancial dice - probably willpower 3 and discipline 1, force rating 1 or 2, my take is force rating 1.
So in total the maximum amount of force points he could ever hope to generate would be 2 due to force rating x2 to cap, 4 if the force rating was 2.
The enviroment is a circumstancial factor in the situation and thus a contributing factor, this could either be a +1 setback or a +1 difficulty.
The self-doubt also a circumstancial factor in the situation, is most definitely also a contributing factor, this would be +1 setback.
Him still being in the early process of learning about the force and thus not have, if so, then it would be +1 difficulty.
Fatigue might also play a part, if so, it would be +1 difficulty.
Fortunately, I don't discourage easily. All I wanted when I posted it here was to get constructive feedback, and potentially some constructive suggestions on adjustments, tweak, improvements and perhaps how to simplify it. Not to convince anyone to use it, anyone are more than welcome to use it if they want to. Unfortunately, some just want to bash at what they don't understand, or bash at it because it's different and not what they like. I though my system would be simple to understand because it uses the game's dicepool system, and basically it's an adaption using the game's dicepool system and mechanics with some rules and mechanics to support it - just like any dicepool system or force dice system has. So if it makes it easier better understand it, consider it more as the game's dice pool system.
I do not seek to convince you about the system, but I tried to elaborate a bit on something you didn't understand with regards to my system.
However, fear might affect their ability to concentrate, but if you remember, fear leads to the dark side. By not letting fear interact with the OUTCOME of the force point generation, then fear doesn't do what it SHOULD do.
All it then does is potentially stop them from doing what they want to do. If temptation for the dark side is as you say in your game, it would make sense to actually make emotions be able to affect the outcome of the force point generation. It may feel like I'm trying to convince you to use it - I'm not, but I'm trying to prove to you and to others reading, this exactly one of my gripes with the force dice, the force point distribution AUTOMATICALLY assumes how difficult it will be for anyone to access the force, regardless of their situation, ability or skills - the only thing that matters with that is getting more dice ups the chances of getting what you want. I personally feel that the predetermined STATIC nature of the force dice interferes with how the situation affects the force users ability to generate the force points it needs. Furthermore, I think the choice of what one wants to generate also plays an important role, and more importantly whether to use the force or not, because the situation could easily be too circumstancial to use the force, like attempting to use while being very afraid.

Even with the force dice can one fail, not just because of choice but because of lacking destiny points, the probability for getting for force points about the same in either system, you can consider the circumstancial dices in my system as a dynamic dark side point distribution.

I hope it makes sense, but I probably have to present the rules by a different format to make them more understandable, even though I do find them easy enough to understand, but then again as I made it I know how it works.

I don't know if this has been resolved for you, but to me it sounds like you think you commit force rating and therefore force dice by purchasing the force power. This is not how the committing force dices work, you don't commit your force dice by purchasing a force power, you commit force dices when you activate it and want to sustain the effects, this will temporarily lock an amount of FR to the force power while the power is being sustained, effectively lowering your FR by that amount until you stop sustaining that force power. 
I hope this help clear some of your confusion. 

Pour everything into a house rule and then have your heart broken when you realize nobody else gives a crap about what you've done. 

Heartbreaker rule if ever there was one. 

So the first and most important question that needs to be asked is "what are you trying to accomplish with this?"
It adds a lot of extra work to what is currently a fairly simple process, and is reminiscent of D&D spellcasters (particularly in pre-4e editions) where they have to do a fair bit of on-the-spot math to figure out the effects of their better spells.  So on first pass, it feels very much like making things more complicated simply for the sake of making it more complicated, when the core systems of the entire game is trying to avoid excessive complications and keep the story moving.
If you're intending to make overall Force usage more powerful and easier to access without necessarily having to dip into using dark side pips, then I'd suggest just drop the whole "roll the Force dice" and just treat a Force user PC as having a number of Force points equal to their Force Rating plus one-half Willpower (rounded down).  It has the desired effect of Force usage being much more reliable, but without slowing the game down.  That said, I'd suggest taking a note from Genesys, and for every Force point utilized beyond their Force Rating, the Force user either suffers 1 strain (light side) or 1 Conflict (tapping into the dark side).
For instance, a PC with Force Rating 1 and Willpower 3 would have access to 2 Force points when activating a Force power, but if she want to use that second Force point, she'll need to either suffer a point of strain or a point of Conflict.  This reflects that younger/inexperienced Force users tend to struggle with performing grander feats of the Force, and that the dark side is the quicker and easier path to power (Conflict isn't nearly as steep a penalty as strain for most characters), but isn't necessarily more powerful.
With committing Force dice, what happens there is the PC still lowers their effective Force Rating, which means they don't have as many Force points available when activating a power.  So to go to the sample PC with Force Rating 1 and Willpower 3, let's say she's got the Sense power with the defensive control upgrade.  On her current action, she commits her Force die to Sense, but on her next action she needs to use the Move basic power to grab a silhouette 0 object within short range.  As her effective Force Rating is 0 due to the committed Force die, she only gets the 1 Force point  from her Willpower, but will either have to suffer strain or take a point of Conflict to use it.  Since she's only got the one Force point, she can't activate any range or strength or magnitude upgrades she might have purchased, but then again under normal rules she wouldn't be able to use Move at all since she has no Force dice to roll.
To allow for dramatic uses of the Force, where a novice accomplishes a feat that would be well outside their league, the PC can choose to flip a Destiny Point which then doubles the amount of Force points they'd have available to them, but also doubles the strain/conflict suffered from using those additional Force points, as such extraordinary effects take a toll on the user.
Now if you want to begin going the route of Force Unleashed levels of Force using nuttiness, then PCs get Force points equal to Force Rating + full Willpower, and they don't need to suffer strain or Conflict to use their full allotment of Force points.  Conflict would only be earned for their actions, but the bar for what does and doesn't earn Conflict when using the Force should be set a lot lower, such as using the Force to attack and cause damage (be it wounds or strain) earns at lease one point of Conflict, as would using Influence to cause negative emotions, while inherently dark side effects such as Harm and Unleash would earn Conflict equal to the number of Force points used.  Counterbalance would be that any use of a Force power (apart from committing Force dice) would cost 2 strain, to be paid after the check is resolved (much how Genesys handles the cost of casting spells, which means that any advantages generated as part of what would be a combined check in the default system can't be used to pay off the cost of activating the power).
Back to your suggested alternative method, one thing that leaps out as a warning flag is the reliance upon Discipline, which is already a key skill for Force users, especially for resisting Force-based effects.  By making it the "casting skill" for using Force powers, you make that skill even more important than it already is, and giving those careers and specs that offer Discipline as a career skill a leg up over those specs/careers that don't.  It might be best to simply create a new skill tied to Willpower, but make it so that the skill by default isn't a career skill for anyone, or that it's a career skill for anyone that starts out with a F&D career if you want Force usage to be more effective.

Because the system is intended to use dice to generate points, which is important in relation to combat and other things, such as upgrades and such.
Just pointing out that, because the dice is made on purpose that way, it actually results in actual game imbalance, that also happen to not be part of canon.

So, if not using dice, how do you propose to handle it?