I know I've been beaten to almost all of these, but hey:
Grand Theft Auto IV - They took out so many of the things I loved from San Andreas, and I couldn't stand the story or characters. Thank God I bought the Collector's Edition.
Modern Warfare 2 - I played multiplayer for a week or two before realizing that I was having absolutely no fun at all. Thank God I bought the Prestige Edition for a hundred billion dollars... ~_~
Final Fantasy XIII - Jesus Christ, thank you, Square, for giving me almost no control over any part of the game. I can't even choose my goddamn party members, or where we go, or ANYTHING? UGH.
King of Fighters XII - There's not even a story. Not even a cheesey KoF story...just a time attack mode. WHY?
Borderlands - The RPG part of the game just doesn't mix with the shooter part well enough for me. If I'm shooting someone in the head, I shouldn't be taking off only a sliver of health because my gun's stats are lower than the bad guy's level. It's still a bullet entering flesh. Anyway, I get the concept, it just doesn't work for me. Thank God I bought all the DLC when it was on sale...
Lost Planet - It looked so cool...how could blowing up huge bugs be bad?! Earth Defense Force 2017 was amazing, but Lost Planet's clunky controls just killed it for me.
Trauma Center: Under The Knife - Those last patients...my God. I have never been so close to snapping my DS in half. THANK YOU ATLUS.