Aye, but how's the game going to handle operations like Overlord and Market Garden that involved huge numbers of bombers
and transports. It's either going to have to short change one or the other at the time, or give the allies 10-15
thousand more bombers over the course of the war than they actually had. If the vanilla game doesn't make the distinction, it has to inevitably mess with the historicity of the gameplay, and not in small ways.
As for the Li-2 VV, how many were produced, and were they in any way comparable with a Pe-2, SM-2, Ar-2 or IL-4? It sounds a bit like using a very limited historical exception to prove a rule. You could use the same logic to say that there's no need to model heavy tanks, for example - the ratio of heavy to medium tanks was far smaller than the ratio of transport to bomber aircraft. Note - I'm not suggesting we remove heavy tanks from HoI

.
I understand the need for gameplay manageability, but it'd be one extra production line for any nation that wanted air transport capability. You could then park them in the supply pool for general play, and pull them out and task them to supplying pockets and doing paradrops as required. For people that didn't use them, it's no extra burden at all, and for people that do use them, they're there. Makes a lot more sense than dropping paratroopers/ out of B-17s, Lancasters and He-111s.
Combining them all together (not PlasticPanzer's suggestion of having transport variants of bombers, which'd work fine) also means that every nation with heavy aircraft suddenly has a capacity to supply encircled troops in a pocket. No more strategic need to have a transport airfleet, just send in the heavy bombers. Even the bombers used in the Berlin airlift needed to be refitted (Lancasters that had pre-blockade been turned into commercial fuel tankers and mid-air refueling aircraft, for example), it wasn't just a case of 'let's dust off those bombers, fill 'em full of jerry cans and send them over'. That's a very real gameplay implication - and given the far greater defensive capabilities of bombers, it means any future encirclements would be far easier to maintain than in previous versions of the game, or the actual conflict.
It's a similar gameplay skewing for paratroops. Gone is the need to ensure a transport solution for your paratroop divisions. As you can simply re-task your bombers to the job, you're upping the effective capacity of every nation in the conflict to deploy divisions simultaneously. Why limit it to three divisions dropping into Market Garden when you can divert the whole of the USAAF and Bomber Command (in the ETO) for a couple of days and drop 3-4 Corps in? You could have Sicily overrun by paratroops (with air support) alone, and without the need to build up a single bit of strategic paratroop capability.
It all sounds very, very exploitable, unless we're taking paratroops out of the game as well. Just mentioning it, as it's probably easier to head off at the pass before launch, rather than try and patch to deal with army groups of paratroopers dropping from the air in the main game.