This is going to be a long post so bear with me.
My group was (and still is), very interested in playing Ascension and as GM I also saw great potential... but not so great implementing of that potential in the book, so over a long period I gradually, with input from my players, began implementing small and sometimes not so small changes to the careers and system as a whole, and am still in progress of fine-tuning these. I will note anything I can remember from memory.
Note: These are changes we are planning to use and I am not recommending that you use them, simply showing them so you can take what you want, if anything.
Dark Heresy/ Ascension changes as a whole
Firstly, use everything that Black Crusade changed (this includes the amalgamation of similar skills, new talents, the much better Unnatural Trait rules and Psychic Powers etc. except the Chaos worship things obviously), any other changes will be noted below.
Skills. We added the third (+30) upgrade to all skill and decided that it could be bought at 100 points more than the equivalent +20 for all classes. Secondly we split each of the Mastery Skills as we found that becoming an undisputed master just like that *snap* was a bit over the top. So instead of getting all those skills at +20 level each Mastery skill function more as a catalogue for which skills are available at that rank, so you can buy any of the skills included at any level (Trained, +10, +20 and +30) for an additional 100 points (so 100, 200, 300 and 400 respectably).
for example: In Forbidden Lore Mastery, the character can buy any Forbidden Lore at any level for 100 points for a trained, 200 points for +10, 300 points for +20 and 400 points for +30. Exactly as if their instead of Forbidden Lore Mastery in the rank there was simply listed all the Forbidden Lores with their respective modifiers at 100 points each.
This serves to limit the Characters from becoming too good and gives them substantially more things to buy, and doing so more selectively. We considered the little problem with space on sheets a minor drawback. If the characters do gain enough skills to essentially having gained the Mastery Skills they can just write that on their sheets instead.
I made one specific change for the Reaction skills (Dodge, and in Black Crusade Parry as well), I changed these from Skills into actions, as such characters (and NPCs) can now no longer increase their chances at dodging or parrying by buying up in them. This has worked like a charm for both Dark Heresy and Rogue Trader as no enemy is impossibly hard to hit and Character are forced to play smarter and more carefully to avoid being killed.
Influence Skills. I have made a few small alterations to Peer. firsly the Good Reputation and Enemy were removed and replaced Peer (1), Peer (2), Peer (3) etc. and Rival (1), Rival (2), Rival (3) etc. like in Black Crusade. secondly Peers now no longer requires you to have any prerequisites. In our game they are also often given as rewards than than bought and should make some sense when buying, (e.g. an Recongregator Inquisitor should not be able to take Peer (1) Amalathians, but a Hierophant could without truble take Rival (1) Mechanicus). I have also epanded the Acolyte Network Influence Talent into an entire sub-system, but I won't go into details as that in itself would take up an entire post.
Talents. Like skills we split the Paragon Talent into their individual components that could all be bought at that rank for their normal price (averaged from the Dark Heresy careers, with GM having the final word).
Traits. A few of the classes have access to the Unnatural Trait, in this case we adopted the Black Crusade system and said that every (x2) becomes (+2) etc. the few career what has access to other traits (such as Fear (1)) had those traits removed from their ranks.
Career Relevant Changes
We have opened all ranks within a career so characters are not restricted to buy anything particular at any particular time, like a lesser version of the system in Black Crusade. This has worked excellent so far.
Furthermore in our game each Throne agent is able to pick from any two relevant career paths (e.g. Our Inquisitor has access to the Inquisitor and Interrogator careers. Our warrior priest has access to the Hierophant and Crusader careers and out psyker has access to the Primaris Psyker and Desperado careers). This however is more a result of our particular style of play and I would not advise it unless the GM things it also suits his/her particular players.
The only two careers I made any significant changes to are the Vindicare Assassin and the Primaris Psyker.
Vindicare. in my game they are outlawed, not because they are too powerful but because to me it makes no sense what-so-ever that a Temple Assassin is part of a Inquisitorial cadre as a permanent addition. However I did make some changes. Firstly with the reduced Unnatural rules and the removal of the bonuses to Dodge the Vindicare are much less of a game breaker, the only remaining problem lies in the Temple Assassin Dodge, I have simply let it be but suggestions include, give him or her half his AB additional reactions instead of the full AB, or ignore the additional dodges and give him or her the equivalent of a force field with a Protection Rating of 35 that never overloads. When this is done the Vindicare is theoretically not that overpowered any more, note: I said theoretically as I have not tested that particular part.
Primaris Psyker. Firstly we have limited any PC psyker's maximum Psy-rating to 6 simply because near godly power are the domain of NPCs, otherwise will be so horribly broken that it won't be fun for anyone. Secondly we changed the Psychic Powers system to work more in alignment with the Black Crusade one.
The full rules are found in black crusade but for a quick summery: a power is manifested by a rolling under the Psyker's Willpower score plus their Psy-Rating (PR) x5 (further modifiers to this test is noted below).
Each Degree of Success (DoS) equals one level of Overbleed on most powers. Range damage powers can be Psychic Bolt (Single Shot), Psychic Barrage (Semi-automatic) or Psychic Storm (Full-automatic), alternatively they can be Psychic Blast (psychic bolt with a Blast radius equal to the active PR).
When manifesting a power there is usually a modifier to the Focus Power Test, in black crusade this is noted in their description in Dark Heresy my players and I have come up with the following system:
Each Minor psychic power gives a +10 to the test, each major psychic power gives a penalty to the test equal to the "tenth" digit in their Threshold (a Threshold 18 power would give a penalty of -10, a power with a threshold of 25 would give a -20 modifier etc.). Ascension Powers follows this but counts their Threshold as ten higher than as stated in the book (e.g. Lightning Arc with Threshold 16 becomes threshold 26 and as such gives a -20 penalty).
Any power that either deals an additional amount of damage equal to WB or a flat damage bonus (e.g. 1d10+10) instead deals an additional damage equal to the Psyker's active PR (1d10+PR). Also anywhere where it says WB is replaced with PR. And lastly any power that fires more than one shot or can affect additional targets instead becomes Psychic Barrage or Psychic Storm powers as relevant (e.g. Lightning-Arc would become a Psychic Storm).
Some of the powers (such as My Will Obeyed, Inferno, Lift, Barrier, Tempest and Stasis Shell) have also been changed in our game but I won't go into that now.
Well I think that was everything, If you can use anything feel free.