I don't like the part where action RPGs have you pick between combat and "key" abilities, as if you aren't going to clown on the AI if the push comes to shove. So you get all the navigation abilities 1/3 of the way through, and all the clever progress opportunities don't matter, because the first one you see is wide open.
Deus Ex nailed it off the bat, with skills drastically changing your efficiency with related weapon/tool, and augs being mutually exclusive (although the balance was trash).