ORIGINAL: Captain Cruft
Just my opinion, but reading the runes I'm really not sure that there is any intention to address this. It's too difficult to do it properly without taking the thing back into Alpha, if you can even apply that status here.
As LoBaron has pointed out, there are "work-arounds" i.e. don't put your entire force in a single hex. Spread out, use the whole map ... Simples.
This may work around the game deficiency in the sense that we'll avoid the failure mode, but it just moves the problem down the stack. Instead of a "massive air battles produce unrealistic results", you instead get "large scale invasions are not practical against a prepared defender".
Historically there were plenty of cases where huge air forces were deployed into very, very narrow airspaces; the allies put 14,000 sorties over Normandy on d-day.
The historical generals did this because things like invasions required massive air and sea support to have a ghost of a chance of success.
So if you don't allow air massing, it disproportionately impacts the player on the late war offensive aka the allies.
This game is already demonstrating that its very, very hard, maybe impossible to launch an allied invasion of mainland Japan against a prepared Japanese player, even *with* massive air support. Can you imagine Greyjoy trying his Honshu invasions with a mere 400 plane CAS wing?