A nationwide pyramid should be pretty easy. NT doesn't really have anything beyond park football, so shouldn't be part of it. Then you can have:
A-League 1: 16 clubs, 30 rounds, 2 relegated
A-League 2: 16 clubs, 30 rounds, 2 promoted (the second team via play-offs), 2 relegated
Championship: 2 conferences x 16 clubs, 30 rounds, 1 promoted from each conference (via play-offs), 2 relegated [the conferences would be divided into North: NSW/QLD/NNSW/ACT and South: VIC/SA/WA/TAS, although experience suggests they will be dominated by NSW and VIC teams respectively]
NPL: 8 conferences, 1 per state. 10 clubs, 27 rounds for ACT/TAS, 16 clubs, 30 rounds for everyone else. Inter-state play-offs determine the 4 promoted teams.
Below NPL level it should just go State League 1, State League 2, etc., splitting up into regionalised conferences as you get further down the pyramid. VIC could keep its current model. In TAS, SA, and WA you would just go with a north/south split and that should be enough. QLD could go straight to a North/Central/South split below the NPL, then to its nine regions.
NSW is the complicated one. Riverina and Monaro should be fully integrated into Capital Football (which would become an ACT & SNSW federation). The north coast and New England clubs should be properly integrated into a NNSW pyramid. And then you have NSW proper. I would suggest three statewide tiers as currently the case (NSW Premier League, League 1, League 2). Then a conference split four ways (NE, SE, NW, SW). And then 16 regional divisions at the base of the pyramid, with 13 of them roughly corresponding to the present metropolitan districts, plus Central Coast, Illawarra and Western NSW as regional districts.
A key element of the pyramid is to cover all parts of the country, allowing clubs representing mid-sized cities (like Ballarat, Rockhampton, Coffs Harbour, etc.) the chance to ascend up the tiers, rather than being stuck with district level football. If they make it all the way to the A-League it would be quite the fairy tale (like Morwell Falcons back in the day).
That pyramid should only apply to First Grade teams (except perhaps for A-League academy squads). Reserve and youth teams should be part of a separate pyramid that tops out at statewide level, and runs on a club championship basis. There's no point getting 12 year olds to fly interstate.