I actually had a pretty similar thought, and someone mentioned it over on one of the Vanguard threads.
I like the directions Dark Heresy and Rogue Trader take the setting (i.e. emphasizing the oppressive and sucky nature of the empire rather than treating that as a positive thing) and how they emphasize insanity and corruption and other unpleasantness.
But I totally agree that the mechanics made me go "yuck" when I read through them. And the preplanned adventures leave much to be desired. That being said, all of the setting information provided is really pretty good - detailed, but leaving you room to do your own thing.
So, on to some practicalities!
I've been thinking about how to make a sanity/corruption system work in AW, and I'm thinking maybe you just treat it as another class of harm. You have the option of taking 'debilities' (phobias, mutations, whatever's appropriate) to avoid 'injury' or 'death' (here being more serious psychosis or mutation or what not).
I also think that the spellcasting rules presented in Apocalypse D&D make a pretty neat fit for psychic powers (with a chance of perils of the warp and/or losing sanity/corruption and/or having crazy warp emanations).
Oh, and all this being said, I'm almost positive that you could play a game set in Necromunda (with the gangs and the underhive and so forth) with zero hacking at all. Except maybe changing the names of some of the weapons. Otherwise, totally perfect fit.
That's all I've got right now. I've put together a pretty good picture of the rules via the development blog, discussions, this forum, various hacks, and Vincent's main blog, but I'm waiting until I have the real rules in front of me to cook up anything concrete.