Relatively easily... the 9 GF winners of each NPL plus 7 of the highest placed (on the table during regular season) "runners up" compete in a round of 16 cup/cl type format and the two finalists go up to the championship (the GF winner automatically and the runner up goes into playoff with the second last team on the championship table)...  

The goal would be to grow this end of year (qualification tourney) into a fully fleshed out Australian championship second division of 16 x clubs over 3-5 years how that is done is the real challenge... My suggestion would be to do work with the clubs that show consistency in making it to this (playoffs)  over the time frame (whatever that is decided to be) to meet the necessary club licensing criteria (I believe FA is already implementing this) and then offer this as a full time home and away league feeding into the championship .. then rinse and repeat for the third tier...  It gives NPL clubs an achievable  path and a realistic time frame of perhaps a decade to get all three levels to a simialr degree of prfitablity and readiness to compete at the highest national level. I dont think we need massive upwards (or downards) movent of clubs bewteen the tieres, just a fair and honest mechanism for which they can achieve this.

My dream 25 year goal is 

Australian Championship - 16 x clubs (maybe more)

Australian Championship 2 - 16 x clubs (1.5 clubs up for promotion)

Australian Championship 3 - 16 x clubs (1.5 clubs up for promotion)

Australian National Premier Leagues promotion relegation tournament) 1.5 clubs up for promotion - 16 x clubs (with proviso that they meet club licensing criteria - some years less, some years none... whatever it is each season)

National Premier leagues - 9 x federations of 16  clubs each ( GF winner gets the option to apply for end of year Qualification tournament)

each NPL then should have NPL 2, NPL 3 and then Sate 1, Sate 2 , State 3 etc etc depending on size and number fo clubs in state.

ALL feeding into each other.... at the very least 48 x clubs, all aligning to FA club licensing criteria (must have TD, womens teams, ALL age group teams of boys and girls, Access to a stadium with 1000K minimum capacity and mens and womens changing facilities and lights adequate to host night games)  Its not that hard to do....  The main issue will be to monetise it so that travel can be  underwirtten at AUS Chamionship levels 2 and 3 and the end of year qualifiactions, everything else can start tomorrow. 

The one main issue I see with our pyramid is the "fitting in" of underage teams to a national framework... This would have to remain as is at state level for all clubs I think, we cant have U13s flying around the country. 

How do u solve the 9 into 1 issue? Such a bottle neck will kill investment. Without a conference it isnt a pyramid its a ladder on a pancakr

Your both so keenly carving up the country into conferences, have you stopped to consider the clubs involved in these state based comps? At a third tier level any club wanting to show a little ambition would want to be able to attract a local following to increase revenue both from matchday advertising and gate takings food drink... This would lend itself better to inter city/state rivalries rather than the Darwin Aces flying into Adelaide every second week...  This fascination with geographical representation doesnt lend itself to meritocratic sporting ambition... Let each state NPL decide it's Champion every year and run a knockout tournament post season to decide who goes UP to the championship, its not hard... if VIC and NSW clubs win it every year there is probably a reason this is happening..... Everywhere else in the whole wide world the purpose is to have the best run clubs rise to the top and we will gain NOTHING by restricting this to protect geographic representation.... NOTHING.

yeah so for conferences I guess you just have to subsidize a western conference due to the vast distances. Would need fa to subsidize it but their budget is 260million. The travel budget for a conference system is probably around 2-3 million dollars a year given the aafc modelling. So I think the subsidizing of the western conference is doable Your second option would work well

A small tweek though,I would go
west with WA/NT/SA fully subsidized by the fa
South with act/vic/tas
north with nsw/nnsw/qld or something like tht

if this is part of the pyramid, a conference system gaurantees more opportunities for teams outside of nsw/vic which is a key worry about p and r (that it would be too sydney/melbourne focused)

yeah so for conferences I guess you just have to subsidize a western conference due to the vast distances. Would need fa to subsidize it but their budget is 260million. The travel budget for a conference system is probably around 2-3 million dollars a year given the aafc modelling. So I think the subsidizing of the western conference is doable Your second option would work well

A small tweek though,I would go
west with WA/NT/SA fully subsidized by the fa
South with act/vic/tas
north with nsw/nnsw/qld or something like tht

if this is part of the pyramid, a conference system gaurantees more opportunities for teams outside of nsw/vic which is a key worry about p and r (that it would be too sydney/melbourne focused)