You know what's infuriating? It's never explained WHY he can't fly in the first place. Is it down to his immaturity? Well THAT can't be right, because he literally hasn't changed ONE BIT over the course of a grand total of TWENTY-EIGHT YEARS. Is it because his wings are too small? Nope, they're MORE than enough. So why would Palutena trust so much into an agent who's capabilities are so limited?
Well, it's not much, but in Uprising there is a bit of dialogue between Pit, Palutena and Hades. Hades asks why "Pitty" can't fly, Pit gets really defensive, and Palutena says something along the lines of "Oh it's fine, his wings just don't work right." (Probably not exact but I'm bad with quotes) So, handicap I guess?
Sorry for double post my computer is being weird today.
I've learned that there are some pokemon who technically should not be able to fly who can learn Fly and use it. I found this out when training up a Dark-type team in my Y-game and I taught the move to a Vulaby for the sake of convenience (also, I do like the move). I seem to remember that according to its pokedex entries, Vulaby "is not able to fly" because it is a baby bird (a young vulture) with tiny wings, a fat body, and either an eggshell or bits of something's skull as a diaper weighing it down.
My darn Vulaby flew me all over Kalos! (Eventually, she evolved into a Mandibuzz, in which flight makes sense).
*Hugs Pit* It's okay. Maybe if you train hard you can learn Brave Bird....