Fallout 3. The game itself was great, but it kept crashing really badly (as in "your computer goes black and you need to manually reset it" badly).
Also Phantom Hourglass, they made the sailing worse (at least it was kinda enjoyable, if tedious, in Windwaker) and had a timed dungeon you had to keep coming back to. That dungeon crawling with my one weakness, roving unkillable enemies, didn't make things better.
Edit: Oh, and Final Fantasy XII. Not bad per se, just had dull setting and characters compared to what I liked about previous games. The combat was...interesting, though.