There's nothing in the rules making it easier to Declare + tag aspects before or against a flying character.
There's very little in the rules that says when you can invoke/tag any aspect. It's assumed you'll be able to figure out extremely basic things like that yourself. It's no less reasonable to be able to invoke/tag Flying than it is to invoke/tag Covering His Eyes.
Magic and other powers are generally balanced against their refresh cost. The question is, is Wings? I think not quite.
Yes, you obviously see wings as far more valuable than I do. You must fight exclusively outside in open fields.
If Wings makes those guys useless (or nearly so) against you, the answer is not to never let the guy with Wings fight them. The answer is to make Wings expensive enough that the usefulness against those characters is reasonable.
Or, you know, let them be easy to beat and not craft them into the story as an epic threat. Myself, if I really wanted those to be a threat to the players, I'd give the zombies, werewolves, red and white vamps guns. Let Sue and the Denarians throw cars at them. Let the fae, and any of the others who can, use magic. Don't make your npcs unthinking targets*, make them an actual challenge.
* Zombies yeah but their master isn't.
Oh, and one other thing: can you do me a favour? Go over your arguments and try to find one that couldn't be used to justify Physical Immunity with a catch of silver being available for the cost of one refresh.
Straw man argument on silver but I'll give it a go for flight. Physical Immunity -8. The Catch +6: +2 only vs melee-ranged attacks, +2 accessible to anyone, +2 anyone will notice immediately. Human Form +1 (Required based on the GM ruling that bigass wings are too large to hide with Human Guise or Flesh Mask). There you go, -1.
Which shows the problem. You have shown that a GM can deal with the effects of Wings in game. But what you haven't shown is that that means that Wings is balanced at its current cost. If you can show that, I'll agree with you. I don't think that you can.
I really don't need to. It's in the RAW. Personally, I don't care if something in the RAW is balanced or even fair. I just take it as a fact of life like gravity and deal with it. If your players don't like it then house rule it otherwise. If you don't like it and they do, deal or piss off your players and house rule it otherwise over their objections.