After thinking about all of this some more - I realized we hadn't talked about air commands and air HHQ like Long range air command. Do you normally leave their support level at 3? What effect does this have - since I'm not sure what support units they could draw that would help other than maybe AA?
I usually assign 1 AA unit per controlled air base to air commands.
Also is Soviet pilot supply usually a problem? I.e. should USSR air force not deploy its "bad" planes - frex the obsolete biplanes - in an effort to save pilots for better planes to come in the future?
Pilot supply shouldn't be a problem, every plane should automatically have a pilot. We used to be able to check the pilots, but that was for debugging purposes.
From your experience, how important it is to fill those Air HQs with AA support units? I have seen a lot of comments about the unprofitability of airfield bombing after turn 1 (for Axis at least), wouldn't that mean that those AAs might not have an occasion to be useful at all?
AA units should fire at air missions moving through their area. You could assign most AA units to regular HQ's, but I prefer to keep a number of them in air HQ's. AA units can be pretty fragile when involved in a battle, especially the battalions.