The Legend of Zelda Franchise: Ok, I love you Ganon, but just give up man. Any game where you're the villain really does seem like the same game (hence why my favorite is actually MM).
Fallout New Vegas: The fact that Honest Hearts isn't out yet XD Ok, for serious though, loading screens, the bugs (which seem to mostly be fixed), anti-climactic ending, and two fickle things: Cass's hat and Veronica's robes. Hideous things on otherwise really good(-looking) characters (in b4 PC has mods for that you console tard: I know, and if my PC could actually run high-end games I would
)
.hack// Series: WHY MUST YOU BE SO DAMN REPETITIVE!!! I want to finish you, but I just can't cause you get so damn BORING >.<
Final Fantasy 9: The plot going completely bonkers near the end (pretty much everything after going to Terra)
GTA4: Nowhere near the customization of Niko compared to CJ in San Andreas. And pretty much the blandness of the visuals overall.