I don't see Vergil as a villain. He does things that will have negative consequences, yes, but those aren't his target. He wants power for means not specified (possibly ending Mundus, which could be seen as a good thing). Means to an end.
He's an Anti-Hero, saying he's a villain because his actions would cause the death of innocents he hold no regards for would make Donte a villain too. --- Can I haz cheezburger?