I don't know about that one... Civ IV had air stacking limits and I found them to be pretty annoying gameplay-wise.
:: shrugs ::
I think the main reason why air stacking in Civ IV was annoying was because tile stacking didn't also apply to land units.
I don't think forcing you to manage which cities the aircraft are based in either limits the power of air units or gives you interesting decisions to make.
Uh, limiting the amount of air units stacked in one tile certainly DOES limit the power of air units.
Heck, it's pretty much the same way that 1upt limited the power of land units in Civ V.
Now, whether limiting air stacking directly increases the amount of interesting decisions is a bit more difficult to counter, because it depends on the details of the air stacking limits.
Personally, with the current operational radii of the various Civ V aerial units, I'd be in favor of air stacking limits similar to Civ IV: 4 air units per city tile, and city improvements can increase that limit.
Why do I favor a 4 unit limit? Because there are too many important combat roles for aerial units for a lower number.
Whereas I think managing how ground units are deployed does both.
:: shrugs ::
I agree that land unit stacking decreases the power of individual land units (if that is indeed a favorable outcome).
However, I disagree that land unit stacking increases the amount of interesting decisions...
In fact, I find that juggling how ground units are deployed under 1upt just increases the amount of tedious decisions in moving an invasion force. How is it an "interesting decision" to have to obsess over whether each amphibious unit actually disembarked where you told them to, instead of aimlessly loafing around for an indeterminate amount of turns?
Now, that said, I find it odd that land and naval stacking in Civ V would be so stringent, but aerial stacking is completely overlooked. If a player has to nitpick about the deployment of their land and naval units with a fine toothed comb, I see no reason why they shouldn't have to do so with their aerial units too.