I think the easiest way to represent aircraft support is an economic one. Air units are expensive, and expensive to maintain.
I think the back end logistics around naval aviation could be abstracted, as that is a level of detail that most folks wouldnt much care for unless they are REALLY into spreadsheet management.
On an operational perspective, most WW2 carriers had their operational squadrons, plus a number of spare aircraft to maintain operational readiness while air frames were down checked for maintenance. Those same spare aircraft were also set for combat replacements for losses. For example, the USS Enterprise and the IJN Kaga both carried 90 aircraft, 72 combat aircraft and 18 spares of all types. And those were both big fleet carriers.
Light carriers and escorts usually only carried two squadrons, plus spares. The IJN Hosho carried 15 operational aircraft, and six spares.
Most carrier operators also carried additional flight crew as "spares". In actuality, the additional flight crew allowed for normal operational tempo, and some replacements. Japan, for example, looked at their squadron command staff as spare flight crews to replace operational losses. (which had really bad results to their flight training later)
Most carrier operators would try to maintain operational readiness by maintaining their aircraft and crew spares.
From a game perspective, you could build a carrier around number of squadrons carried, and type, and then add x amount to cover losses, or you could just build by squadrons carried and assume spares are built into that number. Thats pretty straightforward, and wouldn't be excessively complicated.
As far as the planes themselves, you could assign a squadron to a carrier with open squadron slots until they were filled. When the squadron is destroyed or too badly damaged, you can rotate them out and slot a new squadron in.
There is a sci-fi game called Aurora that has a system like this in place for carrier ops. The system in that game has your design the fighters, build them, then assign them to squadrons, and assign the squadrons to carriers or bases. Its a more complicated system, but that game is a micro-managers dream.
I would be really interested in seeing some of the other aspects of naval aviation and the associated technology be covered. The development of naval aviation tech. At start, naval aviation just had fighters and light bombers, and were not much of a threat to ships and served mostly in recon and anti-recon duties. As the tech changed, you had an evolution in capabilities.
For example;
Naval Fighter technology (starting tech would be a biplane with 1 or 2 .30 cal or 7mm machineguns)
--Heavy Machine guns (US/UK .50 cal/12.7mm for Italy/Japan/Russia or 13mm for Germany)
--Cannons (20mm for just about all, 23mm for Russia)
--Monowing fighters (1920s tech, monwings had better speed and range for same power vs. biplanes, but were less maneuverable)
--
Naval bombers technology
--Seaplanes (1914 ish, Japanese seaplanes bombed German targets in China)
--Light bombs (1910s)
--Torpedo bombers (First operational use was UK vs Turkey in 1915 in the Med)
--Monowing bombers
Naval Aviation Carrier technology
--Seaplane Tenders (Operational use started in 1914, but Seaplane tenders (and seaplanes) were very weather constrained)
--Arresting Gear (Allows first actual aircraft carrier, late 1910s/early 1920s. First actual use was the UK in 1917)
--Light carrier (1920s, 1st real carrier was IJN Hosho in 1921, followed by USS Langly (1922) and HMS Hermes (1924))
--Fleet carrier (late 1920s, 60+ aircraft (5 squadrons) ex. IJN Akagi, USS Lexington)
--Escort carrier (1940s small, cheap, and slow carriers not intended for Fleet use. Mostly anti-sub, close air support, and aircraft transfer) Questionable on what role would be in RTW2. At the same time, there were more escort carriers built than fleet or light carriers by a huge margin. Perhaps they get built like subs and deployed into a sea zone to attack subs and or ground invasions?
--Armored flight decks. (late 1920s. Biggest users were the UK, which made their carriers very tough to sink from the air, as proven by later operations in the Pacific. It did reduce the number of aircraft the carrier could carry for the same tonnage however)
Aviation Tactics
--Long range scout aircraft/scouting doctrine (started in 1910s, but this was a critical advantage to spotting and attacking enemy surface and carrier groups. The Japanese had a huge advantage in this early on, and its the reason that they stressed range on their aircraft so heavily)
--4 plane element vs. 3 plane element (Japan, Russia, and the UK were still using 3 plane elements when WW2 started. This was a serious drawback in operational use and lead to higher losses against opponents who used the 4 plane element. This was particularly noticeable for the US vs Japan, where the US two pair, four plane formation helped offset the huge performance edge held by the Japanese Zero over the standard US F4F Wildcat.
So, that just an example, but there are some real questions that remain. Such as the use of Escort carriers and seaplane tenders. Seaplane tenders were of limited effectiveness, but were pretty critical to getting carrier aviation off the ground. Still, anything other than calm sea states render them useless.
The biggest one would be the aircraft themselves. Personally, being able to design the aircraft like we do now with ships would be really interesting. You could definitely see a difference in the different navies technology and tactics reflected in the design. Just as importantly, aircraft design in the 1920s and 30s was just as rapid as naval design in the late 1890s and early 1900s. The Japanese A5M was the most advanced naval fighter in the world when operationally introduced in 1937, it was the first high speed monowing naval fighter. Three years later it was obsolete and replaced by the A6M Zero fighter.
I would love to be able to design the planes, based around speed, maneuverability, armament, protection, and range. That may be way too complicated for the scope of RTW2, but its a thought.