Neverwinter Nights 2: Buggy beyond what is acceptable in a game. Also, the influence system was arbitrary.
Nwn2, Mask of the Betrayer: Plot holes in the timeline, Kaelyn was annoying if you decided to be a follower of Kelemvor, and the game is quite buggy
Fallout 3: Combat disparity, odd use of V.A.T.S., Having a lot of worthless perks
Pokemon Silver: Graphics and sound were crap, story was odd, PC box was useless without constantly checking back
Dragon age: Origins. Combat was slow at times, the PC was a blank slate to the point of being empty, the DLC items made the game very easy
Dragon age 2: To many specializations were removed, you no longer had the option to stop at chat with your companion no matter where you were,
Mass Effect: The story exposition was laid out far too quickly, and the plot twist did not shock me
Mass Effect 2: There were to many squadmates, they added ammo, and it felt less like an RPG and more of a shooter.
RDR: Controls were horrible, and just trying to walk broke emersion.