Okay, in general this is really exciting and it's clear a lot of good work went into this. You're contributing to the community in a really excellent way.
I'm gonna skip over pointing out all the stuff that goes right, apologies about that. I'm just gonna take a minute and scan for "bad rules text." By that, I mean stuff that's written in a way that it shouldn't. It's either inconsistent with how FFG writes their rules, or it's vague and open to interpretation, or it doesn't take into account certain potential eventualities, or it doesn't correspond to game terminology as the impartial rules read. I think it's clear what your intention is with these cards, but most tabletop gamers want the rules to serve as a neutral referee, so they really can't be left open to interpretation.
Ship armaments that don't have any dice (can't attack) should have an armament of "–" rather than blank.
Hyperdrive (might as well be a keyword) should read something like "When you activate during the first round, increase your speed by 2." Although, personally I'd prefer that the hyperdrive rules interact with deployment, so that you can deploy within distance 1-4 from a ship, rather than within distance 1-2. Think about whether that would break the game with hyperdrive/Strategic squadrons who could vacuum up objective tokens even more easily.
Obi-Wan squadron would be a little tighter if it said "When you attack a squadron without Force Affinity or Droid..."
N-1 Naboo fighters look kinda weak, and I think the Royal Escort ability isn't as interesting as it could be. The marginal benefit of Escort (a semi-weak ability to begin with) that only applies to one or two squads in your list is very much outweighed by the restriction on listbuilding. It's a whole ecosystem of Naboo squadrons that seem unlikely to see play because of how they only work in a certain way. Compare the N-1 (11 points) to a TIE Interceptor squad (11 points) and think about whether the N-1 even comes close.
Palpatine squadron's ability "All other friendly squadrons within distance 1-2 gain +1 hull" is wonky. The game does not include any convenient method for keeping track of this ability, so it seems impossible to implement well. You have squadrons popping up and down in their maximum hull values according to their proximity to this one squadron, and the card doesn't explain how to resolve it. If my squadron is at 1 hull and it flies away from Palpatine, does it instantly die, or does it remain at 1 hull? If my squadron is at its maximum hull value and it moves within range, do I somehow set its hull dial past its maximum value? It's probably better to rework this ability. If it doesn't seem like it's not evil enough for Sidious, perhaps he could just restore hull like the station obstacle?
The V.I.P. keyword for squadrons is wholly untested territory. I can't evaluate whether or not it messes the game up, but it's tricky to add something like this. If it continues to function as currently written, consider changing the wording. Perhaps the keyword needs a number in there, so that some units could have VIP 20 and some could have VIP 10, affecting the points "bounty." And look at the wording of the Most Wanted objective. "End of game" rather than "end of round 6" (not all games go to six rounds), and cleaner wording than a confusing direction about gaining points.
Droid (activating): I'd split off the two rules. The rule for squadrons that can be activated as if 0.5 squadrons can be understood intuitively, but I don't think it holds up to a strict rules reading, which would break down over the undefined concept of "treated as 0.5 squadrons." Also, neatly doubling the number of squadrons activated seems like it will absolutely shred anything: A Providence-class Carrier can casually activate 8 droid squadrons with a single unimproved command, and that's way too good. Better to make it something like "Control Network: When a ship resolves a [Squadron] command, the first Control Network squadron that it activates does not count toward the number of squadrons it is allowed to activate." This way, it just adds one free squadron, so it's kind of like a free Expanded Hangar Bay for each command, but not a free EHB for each squadron. That's still good enough that you should reconsider some points costs.
Droid (the "tribe" tag): I don't think you actually need "Droid" to be a keyword at all. As far as I can tell, it is only a rule in order to interact with Obi-Wan's ability (he can't Mind Trick droids) and the droid-buffing cards of the Droid upgrade slot. I wouldn't bother limiting Obi-Wan's ability like that. For one, other games don't do this such as Imperial Assault or Battlefront II. For another, you wouldn't be consistent unless you also bothered to prevent him from Mind Tricking IG-88, magna-guards, and a few individuals who resist the mind trick like Cad Bane and Mandalorians. But! For the purposes of the droid-buffing cards, you might as well just have them target squadrons with the word "Droid" in the name, just like the titles for 7th Fleet Star Destroyer and Mon Cal Exodus Fleet.
"Activation range" isn't a term in the game, as it's used on the various droid-buffing upgrades. Other similar upgrades in the game just pick a range (medium), and you don't get bonus synergy if you boosted your activation range. If you want to gain the advantages of Boosted Comms, it would be better to have the upgrades work off of actual Squadron commands, rather than just a bubble around them.
Nute Gunray squadron: "towards a friendly ship" is not a game term, and Armada does not give any objective way to resolve this instruction. For this ability, I would suggest saying that the movement must end with Nute in contact with a friendly ship's base, and forget the nonsense word "towards."
Assajj Ventress squadron: "ignore 1 defense token" is not a game term, and Armada does not give any objective way to resolve this instruction. No rules in Armada instruct a player to "ignore" tokens, and it's not clear what it would mean if you were going to do this. Does it mean that the target cannot spend that token, or merely that the token (if spent) does nothing? Better, if not 100% equal in effect: "While attacking an enemy squadron with Force Affinity, before the Spend Defense Tokens step [so that you can't reroll], add one blue die to your dice pool and set it to a face with an [Accuracy] icon." You could tone it down a step by making it work like Captain Jonus, changing a die you already rolled to an Accuracy, rather than adding another die, but it's only a marginal difference given average rolls. Rolling 4 blue dice is already really strong against Force-users (who are all aces with defense tokens), making Assajj already pretty incredibly deadly at her job without making her number of accuracy symbols simply absurd.
General Grievous: You can attack twice, wait what? This needs to be better defined, as nothing gets to simply "attack twice." Can I shoot twice at Obi-Wan? Can I shoot once at Obi-Wan and once at Anakin? In either case, that's so, so strong! (Prior to this, only Jendon or Adar Tallon could allow this to happen, and they were both harder and more expensive to implement than this.) Perhaps: "Before attacking, you may choose to remove one die from your anti-squadron armament until the end of your activation. If you do, after your first attack is resolved against a squadron with Force Affinity, you can perform a second attack against a squadron with Force Affinity." This would make Grievous shred generics with black dice, and flail at Jedi in an annoying but not very efficient way (good at wasting tokens, bad at sticking damage). Pretty on-brand for Grievous.
Wulff Yularen: Unclear if this "you" means that Yularen's flagship gains command tokens, or the ship that discarded its dial gains command tokens. This is Strategic Adviser all over again.
Colburn: The way Armada is written, this commander should refer to spending two accuracy symbols to target defense tokens, not to block them, since the rules don't use the word "block."
Yaw: The rules should increase the yaw value rather than gain an additional yaw value.
Once Per Game: No other rules let you track a "once per game" ability in your head, without physically representing it somehow. That's the reason for the discard or exhaust effect. I think this will have to either be a discard effect, an exhaust effect, or an effect where you place a token on the card.
Half-Health: Armada uses very specific terminology here, and the phrase "half or less hull points (rounded down)" is against the rules, and also unclear. (On a 7-hull Acclamator, does this trigger if I have three damage cards because it's less than half my maximum hull value, or four or more damage cards because you're indirectly trying to get at the idea of having low health?) Hull value, not hull points. Hull value isn't like hit points that go up and down, rather the rules only ever refer to the number of damage cards carried by a ship. So: "...if you have a number of damage cards equal to or greater than half your maximum hull value (rounded down)" is more valid for the game's rules, and it eliminates the ambiguity caused by imprecise terminology.
It should say unequip and re-equip. See the Profundity title. He ain't no Kaminoan.
Obi-Wan commander: Resolve Damage step should probably be capitalized, as well as in other rules like the officers at the end of the document.
Anakin commander: I think it's a mistake to introduce the game's most expensive commander ever, and have him be hyper-focused on winning dogfights that at best contribute indirectly to victory. Though, for Anakin, maybe that's spot-on. But I'm not sure he's worth the price. A lot of fleets already get his benefits in other ways, and they don't even have the limitation on rerolling the same die more than once.
I notice a general trend toward Republic commanders having multiple abilities, which breaks with how the designers write commanders who aren't named Sloane (and her several abilities are more thematically linked, while a lot of these are multiple unrelated abilities).
San Hill: Very unclear. (The concept of -25 victory points is grokkable from an intuitive perspective, but I don't know if it will mesh well with established rules.) Do I get to pick any legal upgrades at all, and bring 425 points to my 400-point game? In his second ability, it seems unclear whether I can only rearrange my upgrades within my fleet, or if I get to swap from any upgrades in the game at all, or if I get to just slap 15 points of additional upgrades onto my already equipped ships.
Shu Mai: If I increase my maximum shield value, and then those hull zones take damage, can I recover shields back up to 6? Because the card doesn't spell it out.
Wat Tambor: Same question as Shu Mai. Plus, this looks like each of my Large-base ships get to increase all of their hull zones' shield values by 3, which is pants-on-head nutso broken (compare to Motti). I hope that's not it, but it's not clear what exactly he does.
Count Dooku: I think you could simplify his ability by just saying "You must choose ships with Force Affinity, if able." Being able to mind control enemy ships and make them shoot each other is probably too good, broken. But this card also opens up a bunch of questions, like: "You said that Dooku gets to choose the targets of this ship's attacks. Well, I decline to declare any attacks, as is my prerogative, so Dooku doesn't get to shoot anything!" Plus, he's another once-per-game ability that doesn't ask you to track his usage. He should be a discard, even though we've never had a discardable commander.
Barriss: Is Medical Team that doesn't ever get discarded and has unlimited potential uses per game. That means she can potentially negate an unlimited amount of damage, depending on how many Crew crits come up. There's probably a price point at which she'd be balanced, but I think she needs to be an Exhaust ability, and I think she needs to be more than 2 points. Also, this is potentially ambiguous if the card dealt would destroy Barriss' ship. Medical Teams has a crucial difference in timing--before rather than whenever--which means that the Crew crit never touches you ship, so you'd live. With Barriss, it looks like you would take the card, then discard it, but you'd never get the chance to discard it if that Crew crit is enough to blow up Barriss' ship.
Whew! That was a lot. I'll give some more feedback later.