Malekith was the only choice for me. There were a multitude of problems with TDW, but the lack of development of the villain was the biggest one. He had no personality, no compelling motivation and a plan that wasn't a plan at all. Even his back story -- his race existed 5,000 years ago, before there was light(?) -- made no sense at all on any level. Maybe the writers are creationists who think that the universe was created only 4,000 years ago instead of 14 billion years ago because there damn sure was light 5,000 years ago. Also, Malekith destroyed his own world, so why was he pissed with the Asgardians again? That movie's plot was so damned stupid it makes me angry just thinking about it.
I completely disagree with the people who said that the Winter Soldier isn't a villain. He is. Brainwashing might give him an out but he's a remorseless killing machine with a higher body count than anyone other than Loki. Bucky might redeem himself after Steve deprograms him via head trauma in CA3.