Mass Effect
Unchartered worlds/MAKO driving sections - sorry, ME may be one of my favourite all time games, but this was a silly move IMO. Boring, repetive and an annoyance to drive.
Bioshock
Vita chambers - removed the whole purpose of survival instincts. I know you can turn them off NOW, but I don't think you could on its day of release when I played it. Anger.
Oblivion
Character diologue. Great concept with interacting NPCs, VERY poorly executed. How to break immersion in one easy fell swoop - have the same voice actor talk about the same thing I heard 30 seconds ago whilst talking to his own voice!
Gears of War 2
Smoke grenades. I learnt to use them, but they are still stupid in how they knock the characters down. An addition that was not needed.
That will be all for now......