Well, I'd be lying if I said I didn't prefer characters - male or female - attractive, all else being equal. If you're dealing with fiction where characters achieve heroic deeds that set them far apart from normal folks, why not complement that extraordinary behavior with an extraordinary appearance, as well? Good looks are the default for heroes: you shouldn't diverge from it without a reason.
That said, "just to be different" is certainly a good enough reason, as are the old chestnuts of realism, marketing, wanting to tell a different kind of story, drawing inspiration from a different kind of cliché, and a whole host of other reasons that are, in practice, far more likely to be applied to the appearance of male characters than female ones, not merely in games, but going back the entire length of the human literary tradition. Beauty is the generic positive female trait, in a way that convinces me there must be a corresponding generic positive male trait that I can't think of off-hand. Competence? Whatever it is, it's something that's only omitted for laughs or for otherwise subverting expectations about the story.
