To me Magneto was a very complicated villain in that i could not really be againstwhat he did. He felt justified and even righteous in how he met out punishment to the world and its governments and i cant blame him. He often said it was War and in War people die so i dont see him as your black and white villain. He may have bn in the wrong when he 1st appeared wanting to steal some nukes and use them but later we find out who he really is as a person as the character is fleshed out and i can understand why he is the person he is. I even feel bad for him as a character that he allowed his hate to consume him turning him into what he hated most and i often think we as people suffer from the same moral dilemma in life in that we often become the monster we never wanted to be when we were innocent children. the world forces us to compromise with each day and eventually sell out our morals and ethical values, how could we not expect to create monsters among ourselves.
2. Mr. Sinister
Mr. Sinister is another complicated villain. I think he is probably one of the most eerie villains in comics emotionally withdrawn he sees people as lab rats to be experimented on. He feels no pity or compassion which allows him to experiment on people human or mutant thanks to Apocalypse procedure on him.