Altitude limit was a thing in for PC pixies in 4e (walk 20' fly 30').
Altitude Limit: You fall at the end of your turn if you are using your racial fly speed and are more than 1 square above the ground.
A pixie could permanently float at a height of 5' and fly 30' in any direction during its turn, however, the pixie would fall at the end of its turn. (Flying creatures didn't take fall damage if the distance was < its flying speed, so practically not a problem unless running or pushed over a precipice.)
The pixie player got some fun movement tricks, thought out interesting combat manouvers, but remained mostly in the same field of play as the rest of the party.
If you use the Aaracokra (sp?) as your model, I don't see any serious problems. Like the Aaracokra (sp?), some challenges will be easier, but that's kinda the point of special abilities (like a Rogue having Expertise with Thieves Tools). If you want to make sure to keep the character in check, make sure to use some underground adventures, where flight won't be much of an advantage.
So far, having a single Aarakocra in my campaign hasn't caused any trouble, despite my initial reservations. There've been a few encounters/challenges that have been made easier by it, but not enough that I'd consider it unbalancing.