I can see the side arguing that this is a skirmish. In an all out war you might have hundreds, even thousands, of men charging into each other.
Yeah, in the end, it's still a platoon sized game, for the most part. That's still a skirmish, really.
But it's really not even the size of the armies, it's the battlespace. Fliers, even most helicopters (since you don't just hover in place while engaging ground targets with anti-air capability), would be covering far more than the average table size in the space of seconds.
But, in the end, it's just the implementation that has put me off to fliers. They aren't very well balanced into the rules, and were introduced to haphazardly that some armies have really good models, and others don't.
Oh, and the Space Marine fliers are just ridiculously awful looking.