There's only one big problem I can see with this idea. How would we explain why there are two different moogle designs in one game? I believe the answer could be something as simple as a common ancestor with two different evolutions. The moogles of Moghome turned out one way, and the moogles that would be playable turned out another way. There are other ways to address this.. that is just one idea.

I think the other problems would be minor and easy to address. We could say playable moogles lost the ability to fly during the course of their evolution, but retained their wings. That would eliminate any design/lore problems with having a playable character being able to fly.

Would anyone else love to play a moogle? Since Stormblood just came out, the next expansion must be very early in development, so if SquareEnix hasn't made up their mind yet as to what, if any, the next race will be, now is the time to try and persuade them one way or another.