Psykers or Blanks are one example. Tech-Priests, Sororitas, Space Marines, are others, and the line doesn't end there. All these classes come with a variety of unique traits or abilities, and whilst I believe they should remain unique, I also believe their implementation should be balanced to each other and "normal" characters of a suitable equivalent power level.
I'm still an idealistic fan of the concept of a unified ruleset that would allow all sorts of characters to exist in the same campaign (like GW did with its d100 Inquisitor game), because in the end, all these characters can be heroic protagonists exactly like the ones appearing in various stories or other setting background pieces. I'd hesitate to bring up Black Crusade once more, but it still serves as the best example for how lack of balancing can create a ridiculous gap between individual player characters of the very same role, and ultimately force some of them into becoming sidekicks for the others in spite of the group's original ideas. Just look at the altered Horde rules in Tome of Blood and how they effectively introduce two tiers of realism depending on the type of character you're playing!
For DH2, it is somewhat less of a problem now , as Marines aren't available as a class yet, but you can already summon them as Reinforcement Characters to completely steal the show of any of your combat characters, and if DH1 is any indication, it's just a matter of time until some supplement will make them playable here, too.
Over the time, a lot of band aids have popped up to adjust and curtail the efficiency of such characters (revealing that the designers are apparently quite aware of the problems they cause), but as long as the core mechanics remain sacrosanct, I don't believe in a somewhat level playing field any time soon.
As for your question regarding what I would do: I believe both the XP system and Aptitudes are good -- it's the effects of the stuff you can buy with them that need tinkering. Like in any MMO, the more Talents and Abilities you allow to stack with each other, the more ludicrous things can get. Just search the Deathwatch forum for the "1 on 1 vs a Bloodthirster" thread, though lately there's a discussion over at Only War as well regarding clever use of Orders that will see a simple lasgun put plasma weapons to shame.
In short, there's just too many things modifying your numbers. It is unrealistic, it is unwieldy, and it needlessly increases the difference between the characters on too many fronts. It's like the system is breaking down under the weight of its own rules as mechanics, counter-mechanics, bonuses and contingencies all come together, so much so that it has apparently become a sport on these forums to find the most efficient (read: ridiculous) combinations.
But as you mention progression, let me also reiterate an earlier suggestion that this system should perhaps take a page from Shadowrun when it comes to Knowledge skills. This, not Social skills, is what really irks me in regards to the aforementioned tough decisions. Because very few roles require the character to shine in social interaction (the ones that do are usually specialists that come with appropriate bonuses built-in), but many characters end up missing Lore skills that, by all rights, they should have simply due to their origins and past experiences. How come an Adeptus Ministorum character doesn't have "Common Lore: Imperial Creed", for example? Why doesn't a Highborn character start with "Linguistics: High Gothic"?
This is actually a new flaw in the system that came up only with DH2 and its streamlined character generation. I really, really like its modular style, but there seem to be so many things missing that you have to buy extra for precious XP for a proper portrayal of your character, and of course these XP will later be missed for combat stuff.
My idea here would be to expand and rework Lore Skills into a more comprehensive list, where exclusive Scholastic and Forbidden Lores (which could otherwise only be acquired by playing) would be part of the package you get from chargen modules, and Common Lore Skills are made available for a free one-time pick at the value of the character's Intelligence Bonus x2.
Perhaps this would have the welcome side effect of making Lore Skills more relevant in the game as well, by providing a much larger list to pick interesting subjects from, and allowing players to create custom, specialised Lore Skills (with GM vetting) suitable to their backgrounds. For example, an Arbites character from Scintilla would know a lot about the gangs there, but not so much about the criminals elsewhere. Here's an ideal opportunity to increase the difference between individual characters without letting one look more or less important than another, depending on how often you as the GM would insert opportunities for the players to make use of their characters' knowledge, ultimately supporting party dynamics and roleplaying, and players actually thinking about their characters' past.
I've just been playing Shadowrun again the other day, and I can say that my biker's area knowledge of "Bars in Seattle" came in handy at least once!
[edit] This seems to have gotten longer than I had intended -- apologies for that. It's late and I just started typing, with my fingers stopping only as I had emptied what was going through my brain right now. I hope the text isn't too messy.
Edited by Lynata