Ah, so that's where I must have misheard the flying=bird from. I'd seen it referenced somewhere but never bothered looking for the full details about it having been scrapped in production. Anyway, as I said before, Gamefreak knows what they're doing when they type Pokemon, so they gave Flying Pokemon that type for a reason.
Just saying "replace it with levitate to free up the second type" doesn't really do anything. Levitate only protects Pokemon from Ground moves, Flying has a number of weaknesses and resistances associated with it, changing how it's played. Also, that would eat up an ability slot (Gyarados's Intimidate/Moxie, for example, or Tropius's Harvest/Solar Power/Chlorophyll, Mantine's Water Absorb . . . you get the idea).
It isn't like they "gave up" a second type to replace it with Flying (or whatever you would prefer the type that flies to be named). I personally don't mind the name "Flying" for the type, but really, no Pokemon were mis-typed in the making of the games.