It's why I prefer Alpha Protocol to Mass Effect 2. ME2's gameplay may be better (save for that whole planet scanning crap), but the overarching story is garbage and does a lot of damage to the universe established in Mass Effect 1. ME2's ending left me going "what the fucking fuck was that?" where as Alpha Protocol's left me going "Holy shit!!!" (all three times even).
The fact that people panned Alpha Protocol just because the gameplay was mediocre shows me just how far the RPG genre has slipped.
Go do another playthrough and don't use any of the OP abilities. You'll find your experience will vastly improve.