It's an interesting conundrum. MegaCharizard could very well have been a Fire/Dragon type and made fanboys happy but it would have to waste that ability slot for Levitate. It wouldn't have been that much better and now its weakness are more varied. This is in contrast to drought which is a great ability and would make MegaCharizard actually useable in the metagame.
I honestly don't care. Besides, I think it might have something to do with the fact that Game Freak has never changed a dual-typed Pokemon's typing. If it were only Fire and not winged, I can totally see them adding the Dragon type.
By the way, isn't going to be strange having a Butterfree or whatever in sky battles, while all winged Bug types that aren't part flying will be left out of it?