flying PC
If the PC actually uses the wings to fly, it would be a great strain thus limit him to five minutes a day per constitution point if he's just normally flying from point A to point B. Limit that even more if he's using those wings in battle, perhaps the spread would be five rounds per constitution point. This also limits him to how far he can travel in any given day, which I have a bigger problems with over his benefits during combat.
Force him to take additional feats, skill points in order to effectively use those wings in combat maneuvers. Fly-by-attack, airbourne combat, etc...
Have an enemy cast curse on him: sorry, wings are now useless ... and, don't forget have a happy landing!
Constantly have small avians dive attack him from the back. Won't do great damage, but it will bother him like crazy, and force him to make concentration checks. (Great for spellcasters.) If he asks why: the bird-god drove them to it to punish the interloper.
My players learned long ago, better to play a mistructed tiefling than a beloved celestial. Holy ones are constantly bothered by NPC's asking you for favors, handouts, blessing, holy relics, quests, heals, ad naseum. And if you play a neutral or evil celestial, every level past fifth there is at least one chaotic good celestial who has heard about your exploits and wants to bring you back to the Olympia to teach you a lesson...and because they are chaotic, they will be watching you, and will wait until you are weakened, tired, out of spells, sleeping, in jail, etc...to come for you.
Or the most sickest, cruelest, sadistic thing any DM can do: reason with the player! Admit to the player that YOU as a DM made a mistake. (Yes, even using Rule Zero, DM's do that!)
Ask him that in fairness to the other players, that he create a new character, and you will work with him to create another cool, but fair character. I haven't had a player yet say no to me when I do that. ..players want to have fun and be cool and not just create more problems. While they might groan about it, most are willing to oblige.
Hope this helps.
Dren