Most of my choices have been said.
Yu Yevon, FFX, was pretty pointless. Also the fact that it was impossible to die when fighting him.
Necron from FFIX. Not mentioned at all, then suddenly "oh hey I hate everything etc". Then again, there are a lot of enemies on Final Fantasy, and I am sure other JRPGs that are similar. You just happen to be in the wrong place at the wrong time when they pass by.
Shepard, MW2. I've tried to work out why he did it...something about being pissed off at the nuke in MW1 (poor Jackson) but it kind of got a bit extreme.
Both Team Aqua and Magma were ridiculous from the Gen 3 Pokemon games. I mean, Rockets were the original - they wanted money. Galactic wanted to do something with time and space, but they were also quite evil. In fact, both Rocket and Galactic actually injured Pokemon. Aqua and Magma were just awful, and their goals were ridiculous. Also, depending on if you got Ruby or Sapphire, one of them was good so...yeah (whereas on Emerald both are 'evil' but still both suck...oh, and they reform at the end. Good for them).