In WWII the 2nd AIF was raised to send troops to support Britain as had been done in WWI. The Militia, which had taken on the identities of the 1st AIF was, initially, restricted to operations within Australia and its territories, what if the RAAF faced the same restrictions? New air elements would have to be formed specifically to support the 2nd AIF and the RAN while the existing RAAF was restricted to Australia.
There were RAAF units formed under RAF control but my thinking here is the existing squadrons would be restricted to operations in and around Australia with the airpower requirements of the 2nd AIF being met by new Aviation Regiments of the newly formed Army Air Corps, with one regiment being numbered and assigned to each division, in the same fashion as the Cavalry Regiments were, i.e. 6th Aviation Regiment to the 6th Division, 7th Aviation to the 7th Division and so on. At the same time the RAN FAA could have been formed, initially to provide ships flights, training and logistics, but later stretching into carrier operations.
The Aviation Regiments would have comprised of a number of squadrons, including fighter, attack (perhaps dive bombing), reconnaissance, liaison and transport, maybe even a medium bomber capability. This would have worked out quite well as the structure could have been duplicated for the Militia divisions, while the RAAF could have concentrated on continental defence, not only air defence, but also anti shipping strike, general reconnaissance as well as more traditio9nal bombing.
I actually like the idea of the 2nd AIFs Divisions becoming more combined arms in nature, Cavalry and Aviation Regiments, but also replacing one of their Infantry Brigades with an Armoured Brigade. The idea I am toying with is they become more rounded and flexible like a Panzer Grenadier Division, or a modern USMC Marine Expeditionary Force (but not specifically amphibious).