Well according to the official list of Pokémon that can learn fly, Butterfree and the other bugs aren't meant to learn it after all, so I might not put it in actually. I've included all the Pokémon that are obtainable in the game at this point that can learn fly, omitting some of the less common ones that people won't have until much later and first-stage evolutions. Some of the Pokémon to get the Fly License are subject to Career as well, for example only Criminals can get a Xatu, so only Criminals will be able to apply with a Xatu*. Same for Researchers with Swellow* since Taillow is only found in New Bora, a Researcher-exclusive area. So far, I've got:
Fearow, Unfezant, Skarmory, Golbat, Crobat, Xatu*, Swellow* and Honchkrow.
And, for CUT (I intended there to be not as many to make it a bit trickier);
Absol, Nidorina, Nidorino, Nidoking, Gligar, Sandslash, Raticate, Parasect, Weepinbell, Venusaur, Scyther.
I did think about maybe releasing a Version 2.5, with just the graphical update and not much new actual playing content, but I thought it might be a bit pointless since there's not much more to do lol.