This is (sort of...) my gripe with Disney's The Incredibles. The villain is a normal/non-super guy who becomes a phenomenal engineer/mad-scientist-type presumably through hard work and education. And he's the bad guy, while the people who were born special/super are the good guys.
Hah, yes, my point was that they could have made such a character a hero, and the villain could just as easily been a super-turned-evil. (Sorry if a missed a whoosh...)