I think this could maybe only work for subs to an extent, since it makes more sense than having fixed convoy routes (so convoys don't re-route based on threat) and subs that constantly need to be told to move elsewhere when surface fleets appear in the area and it's just not that important to have submarines represented with real units because of their limited usage for convoys, plus the always big problem of deciding whether to use them individually or in flotillas, while in reality each sub should have its own leader, but, for Germany, for example, have the different subs co-operate in wolfpacks when the situation requires them to do so, otherwise hunting on their own discretion.
But air force? As mentioned, it ruins any creativity - you just boringly set some planes to an area, you don't make decoy attacks, don't focus on specific industry of the enemy, don't have individuality in your units (so having an air wing survive from 1936 till 1945 and become legendary for its war tales would be impossible, ruining a very nice aspect of the game that just turns it into a chess game with no background or story), can't take risks (ex. the enemy has an important transport airfleet in an air base and you urgently need to get rid of it before the enemy's paratroopers are fully organised, it would all go under an abstract "Bombing" mission), can't focus your air forces on specific areas of a theater (just have them all over, even if you'd need them more towards some specific contested provinces not in the middle of France bombing rebels, also how would it work if a country only holds a few provinces in a theater (and has no bombing interests in hostile territory) - you can't just add it to one of your bigger ones, but have to seperately set air forces to it, so if you add too few - the enemy will be destroying you, but too much means you're wasting those forces, while adding them to an existing theater would still let you have large force protecting it, but also protecting a larger area etc. flaws).
Damn this wall of text. Apologies, still a bit sleepy so my text is just a big sticky chunk of opinion with no organisation, but IMO my points are still valid on the most noticeable flaws of this abstraction idea.
But what concerns me the most, again, is the loss of individuality. I always loved having some favorite divisions in HoI 3 that I would take to the most important parts of the action, they would gain more experience than others, I would always remember their name and it would be something powerful. So you could actually have divisions that were more known during the war like in real history because of their extended use and whatever else, losing this aspect for the air & naval systems would be really bad. And as I said, IMO, it just turns this really fun RTS into a chess game, which has no story, no background, no context, just a bunch of figures fighting each other by some set rules, each battle being the exact same, just with different decisions. Don't get me wrong, I like chess, but I'd rather have this video game different from chess.