The long flight animations for aircraft do bother me, but they're tolerable.
My suggestion to resolve the problem is to speed up or skip the flight animation using left-mouse clicks. For example, if you click the LMB once during the flight animation, it speeds it up +50-100%; so you can still see it, but it's quicker. If you double click the LMB it ends the animation immediately -- the aircraft returns to base, the damage inflicted and taken flashes on screen as usu, and the next unit becomes active in the queue -- this would dramatically reduce the time it takes to use Air units in Civ5.
I think this would be a elegantly simple solution that would require minimal effort to program and patch into Civ5, and it wouldn't require turning on/off Quick Combat or 2D view.