actually splitting up into theatre modules does not make mission building that much harder IMHO;
there simply were no German/Italian types in the PTO (with the exception of some very very early Italian stuff like the BR-20 bomber or some fighters) and equally, no IJA/IJN aircraft in the ETO;
you also do not need many USN aircraft, in fact all you need is the F4F/FM-2 series, the Avengers and some Hellcats to cover pretty much every combat mission, the USN undertook in the ETO;
for the British, we have the Corsairs, Martlets and Hellcats in their own slots of course;
also, the Russian aircraft types can be thinned out for a PTO module, as there is only a need for the early types (Nomonhan) and the late types (Manchuria); all the in between birds are not really needed;
the minor nations can be split up just like that - no Polish birds in the PTO for example while the Dutch did use different types in the defense of their homeland and in the colonial wars in the NEI...
and the best part of it - in its current state you can add and remove aircraft from BAT by simply adding their respective line in the air.ini or deleting it or remming it out...
this is valid for the stock plane set of WAW - manual additions still would need to be added or removed via the accustomed way....
same holds true for ships and maps...