I've GMed Rogue Trader before, and I'm familiar with Adeptus Evangelion. Evangelion happens to be my favorite anime, but I'd certainly be tending to run rather grim in attitude in general, since I have a bad habit of taking PCs a bit closer to the edge than they might prefer.
The scenario I'd want to run would be an alternate universe with a new NERV fortress city, with an alternate universe geo front, focusing on a new set of alternate angels invading Earth.
I'm not sure how much of the Adeptus Evangelion rules would be appropriate to the game, but I'll re-read the book and figure out how much of the system I want to use. Ideally, most of the focus should be on relationship mechanics, sync ratios, and modeling the psychological disintegration the EVA units cause, though there likely needs to be some amount of system for the giant robot fights.
When it comes to the battle inside NERV, however, I think that using a roleplaying system would be innapropriate, since it basically boils down to "If a soldier gets to shoot at you, spend a fate point or die."