Since all our suggestions to (essentially) nerf it in play by being a more creative GM have fallen on deaf ears, I'm beginning to think the reason Discipol is so passionate.... is because he's a pure melee build in a game with a flyer, and it's starting to tick him off.
In which case, he needs to direct his GM here, and/or provide his character a little more flexibility.
We've given all the reasons in the world why, if flight is so ridiculously overpowered, it can be limited, trumped, or outright nuked. Frankly, the fact that it provides (occasional) (limited) immunity to melee-only characters isn't worth much in a world where such individuals are RARE.
I mean, really. If you live in an area that allows Conceal/Carry Weapon liscenses, how many CCW's do you think are walking around with a hidden knife instead of a gun? Even in Dresden, where the balance is a bit more fantasy and a bit less real-world, most of the things that use melee dominantly do so because they have other edges along the lines of enhanced speed or strength...
In which case, it becomes moot, because I can, offhand, think of a dozen ways they can overcome the already occasional limitation.
Why can't the speedster roll athletics to rebound off a dumpster or car, and jump a zone up... get a single solid hit or grapple in, and boom. Wings useless.
For that matter, if he needs to, I'd allow him to do it without a roll, if he spends a fate point to temporarily have flight (per temp. powers rules), Fly for 1 round representing a jump.
The powerhouse can throw anything, or use a telephone pole that reaches into the next zone up (a little unorthodox, but I'd allow it).
Course, the flyer could go more than one zone up, but then there ought to be some SERIOUS ranged penalties- and at that point, how is he any more overpowered than the pure mortal sniper, who always sits a zone or two away, in stealth, with a high-powered sniper or hunting rifle? He's also immune to melee, capable of reaching out and touching someone from far enough away that even if noticed, whatever came after him would have to get to him AND find him... and he's doing it all for a [+2] (pure mortal) and a couple decent skills (guns and stealth).
Should we nerf him?