Scenarios are an attempt to give people a taste of the historical fighting as best we can manage, using what is available and making consessions to playability (since, of course, without that, we'd have no players). Thus, no scenario is perfectly realistic. But if you get done with a fight, and think to yourself, "Man! That was like this mission I read about!" -- and if you had fun -- then the scenario is a success.
To skip a scenario because it has plane substitution strikes me as missing the forest for the trees.
Availability of planes is only one item among many such as having GPS in the cockpit, not having to worry about weather or much about visibility compared to real life, not having to worry about death or injury or physical endurance, not having any physical problems at extreme altitudes, never any 6-hour missions, no battles set up for 10:1 odds, planes always being 100% maintained, ammo and fuel always being good, full knowledge of what you are up against and when, and sides being balanced so that each side has its chance to prevail.
Also, AH has an excellent and impressively large list of aircraft, but it can't do every single one that served in WWII. If we were to restrict ourselves only to battles where we needed no plane substitution or deletion at all, we would run no Battle of Britain (lacking the He 111), no Flying Tigers (lacking early-war Japanese stuff), nothing in North Africa (lacking some Italian planes), nothing in the Mediterranian (lacking things like the Beaufighter and some Italian planes), nothing on the Eastern Front (where 80% or more of the European fighting of WWII took place, by the way), no Coral Sea or Midway (lacking the TBD), etc.
As an example, what is the most-realistic scenario? I think it's Coral Sea. Similar number and type of ships as history, same number of pilots on each side as history, as close to weather of those days as can be crafted in the game (moreso than any other scenario), and all the same plane types as history -- except that we use the TBM for the TBD. It's a significant change, yes, but still overall Coral Sea has fewer deviations from history than others.
Of course, I realize that there can be people who like a particular scenario but not another.
Me, though -- I like them *all*!