It seems to be common wisdom here that characters should be able to fly from 5th level onwards.

I'm wondering if instead, that should be phrased as "characters should be able to defeat any flying enemies from 5th level onwards".

Wizards, of course, have their fly spells. And you can give any class boots of flying and flying carpets and whatever. But if you are aiming for any story that approaches traditional fantasy stories, you can't really have flight.

So, instead...

We need a way to attack beasties in the air, and if necessary, bring them down.

Just about every class has a ranged weapon attack, even if it isn't quite their optimum attack. So the first issue is solved.

Stopping a flying opponent is trickier. I'm not sure it should be a requirement though -- any monster with a faster land movement rate (or faster swim in aquatic areas) creates the same conundrum but no one says diddly about them.

So, how about this...

Any hit against a creature that needs to concentrate to maintain flight (winged flight, essentially) may temporarily lose control resulting in some loss of altitude. They must make a Reflex save (DC 10 + damage taken), and loses 5 ft of altitude for each point the check was failed by; if this knocks him to the ground, he also takes falling damage.

3.5e removed the high jump caps from 3.0e. Even so, jumping is still too limited to allow for cinematic jumps to make melee attacks against fliers. Since we are aiming for a less animesque style though, that wouldn't be appropriate.

Are there any other ways to counter the obvious advantage that flight gives in combat?