The sympathy-because-of-persecution theme probably shows up more in teen transformation movies, particularly those designed for girls (but possibly boys as well). I think Princess Diaries works in that trope -- the movie, not the book. It's usually a Cinderella story sort of theme: I'm so sweet and good and kind and everyone is mean to me. I'm getting comments about this on my fb page as well, and someone there made me think that maybe what we're seeing is the root-for-the-underdog theme -- because the nerd villains that are showing up in the examples I'm mentioning seem to never win.

Good point about the UF stuff, too. I am surprised that the anti-hero theme didn't occur to me there, given how much of that genre I read! Maybe there's just less clear good vs. evil in those settings, so even the villain might not be really a villain while a hero might do some pretty awful stuff... I'm going to have to think about that!