The main issue is really the fact that the A League isn't run as an independent entity from the FFA. The FFA's stakeholders are not the same as the A League's stakeholders. The MLS works with a franchise model spanning 2 countries and I bet the Canadian franchises will never be the high metrics glamour clubs of that league either. The difference is that the MLS is run by the franchise owners, not US soccer.
A stable, financially viable A League is in the long term best interests of Australian football, and the Nix undoubtedly contribute to that goal. However, the guys in charge of the FFA don't actually give a shark about the long term, they want to please their stakeholders now so they can get re-elected or keep their jobs, and that means when Aussie football people say "kick out the Nix and put a team in my town/suburb" then the FFA goons feel like they have to listen or they lose support for them in their roles.Even if a new team wouldn't be sustainable and would cannibalise another pre-existing franchise.
IIRC the AFC/FIFA recommended that the A League should be run by a separate body anyway, but the FFA didn't listen.