Not really sure if you can classify ANYBODY in the series aside from V.V. as an actual villain (seen as they were fighting for what they believed to be right and what they felt was the right thing to do in their hearts), but I'd have to go with either Schneizel, Gino, or Guilford from Code Geass. I loved Schneizel to death, like Cornelia said, in time of peace he would have made an excellent king. No doubt in mind, and Gino was just freakin awesome man. And come on, look at what Guildford did throughout the series, if that's not loyalty idk what is. Come to think of it, Jermiah was freakin beast too, and I absolutely loved his story.
hmm.....I guess if I had to say anybody that you could think was a "villain" would probably fall in my list of favs from that series. <3
But we'll just stick with Scheizel, that freakin genius of a human being.