Hrm. I guess that's true. But I don't think it's that they're the villain that I find odd, per se. It's that they're a villain protagonist. I don't see that many villain-as-protagonist stories outside of this genre (and maybe the Western anti-hero) -- even in fantasy it seems to mostly be done in parody, or in an ambiguous moral context (as in skzbrust's Vlad Taltos books). So while one story of "Identify with me because the way I was persecuted by jocks when I was a kid has driven me to becoming a super villain" worked for me, seeing it in several places makes me wonder what's going on to make this story worth telling.

Does that make more sense?