Aizen is evil, but I thought the way his plot ended up in execution was a little mechanically written. Especially the part about Tousen randomly joining him at the end to avoid incontinuity. Also, he just seems greedy and cunning, not so diabolical.
Yagami Light from Death Note was pretty heartless, and of course brilliant. He used everybody and everything he could to his advantage, usually destroying it/them in the process.
He really did start to think he was God. After all, his own hubris brought him down. It would have been simple to foil N's plan with a backup plan, even if the real notebooks were somehow switched.
I guess not exactly anime, but Slade/Deathstroke from the recent Teen Titans show was pretty evil. He didn't just want power, he wanted to subvert the opposition. Considering the nature of his universe, he could just destroy his enemies, but there are alot of in universe superheros, and someone else would just take their place. Subversion or breaking the spirit of his enemies would be a bigger blow, especially Robin, who was single-minded. He knew what he wanted, it was evil, and it was effective. Also, he was a master of mind games.
I think the problem with alot of anime villains is they get too convoluted. Plots reach a level of absurdity, and in some case(see Naraku), it doesn't even seem to be clear what they really are even after, despite the fact that by that point it should. Why does every plot have to involve something like destroying the world by launching J.S. Bach into space with a doomsday organ?