You're making the mistake of trying to please every place at once.
I'd suggest any national second tier comp should be pegged to the same number of teams as the NRL to allow every team access to excess NRL players. By ensuring every club has a one to one affiliate with an NRL team you also ensure that every team gets a similar level of funding from an NRL team. This would mean that as the NRL expands, the second tier comp also expands - starting at 16 teams in 2012 and probably expanding to 18 in 2013.
The thing to keep in mind is that by keeping the second tier clubs as separate entities and just having affiliate arrangements with NRL teams, the location of the second tier teams doesn't need to mirror the NRL. There's no need to have 9 teams in Sydney just because the NRL does. Another team in west Sydney that is over shadowed by three existing NRL teams doesn't help the game nearly as much as Perth or Cairns teams in the second tier. Who affiliates with who is left open to the teams themselves to create competition for affiliate arrangements.
So you might start off with 16 teams in 2012 based largely on the Queensland Cup...
Souths-Logan, Brisbane Norths, Wynnum-Manly, Redcliffe, Brisbane Easts, Ipswich
Sunshine Coast, Cairns, Mackay, Tweed Heads, Central Queensland
Auckland Vulcans, WA Reds, Newtown, North Sydney, Melbourne 2
Then if the WA Reds move up to the NRL, three new teams in 2013 to bring it to 18...
Wellington, Adelaide, Albury-Wodonga
Then if say Wellington and Sunshine Coast move up to a 20 team NRL in 2018, then four new teams to bring it up to 20...
Toowoomba, Mid-West NSW, Christchurch, Perth 2
The point is, we don't need to fill every market on day one. As the NRL expands the second tier will also expand, opening up new opportunities as the number of teams increases. If the NRL starts looking to the second tier for new teams then as sides move up, even more opportunities will open to fill the place of the team moving up.
Leigh.