Oh I'm sorry baby, did all my science just turn you on. My bad.
Lol, sorry, couldn't resist.
So here's my maybe, sort of, kind of villain. He's one of the scientists who keeps Locke and Co under surveillance. (Though he's pretty messed up himself and is hiding that fact. This isn't so much a "one day I will have powers too!" sort of thing, so much as a fear that he really has a hard time dealing with, and thus doesn't face. He just pretends its not there.) He's not really evil, or wicked, or nasty, in fact I find him pretty likable. He's really just the antagonist. His reason for keeping them locked up isn't really dark or perverse, he's doing what he's doing because he genuinely believes that it's going to help people and it's not like he's some cruel, dark jerk to them. On the contrary, he has a wierd kind of "we be bro's" relationship with Locke.
The mad scientist thing is even kind of a running joke in the lab. He's young, a bit headstrong, and more likely than some of the other lab workers to take more drastic measures or steps in experiments. He's very "means justify the ends" about things, and that's probably his biggest flaw, the one that really makes him function as an antagonist. He's a little more Inspector Javert than Lex Luthor.
Don't get me wrong, he does do some pretty ass-hole things in the series, there's some stupid stunts he pulls, and he does kind of deserve a good ass-kicking at more than one point, but as far as his motivations go, they are genuinely good...he's just not really the right sort of person to be carrying them out.
And yes, he is a TOTAL ladies man...There is a chance he may have used science to achieve that...but, we'll just talk about that later.