Game Freak logic really is the best answer you're gonna get. Just because a Pokemon has wings doesn't mean it's going to learn Fly. Pidgey can learn Fly because it is a bird, which I feel is very logical as, y'know, birds kinda do that sometimes. Also, if Scyther could learn Fly, Scizor also could, for reasons that are obvious, though I don't think that has anything to do with Scyther not learning Fly. Game Freak has made decisions that are more questionable.