Deus Ex had an incredible atmosphere and a surprisingly good plot, but it was the skill and augmentation system that really defined it. Of course, if I was to play it again now, I'd activate an augmentation cheat.
I was sort of hoping that Alpha Protocol would pick up the torch while bringing other aspects into modern times, but it seems as if Obsidian decided to also borrow character animation and other less than awesome things from Deus Ex.