The Japanese football association's 100 year plan addresses those problems as much as it's humanly possible.
Football purists in Europe hate the Japanese football pyramid, but it's much more successful at promoting sustainable growth than either the traditional pyramid or any licensed/franchise system I've seen.
The growth soccer has experienced in Japan since the early 90s is insane and it's totally down to the 100 year plan, their pyramid system, and excellent administration. It's been so successful that other sports in Japan (RU for example) and other Asian football federations have been copying it.
https://en.wikipedia.org/wiki/Japanese_association_football_league_system
https://en.wikipedia.org/wiki/J.League_100_Year_Plan_club_status#100_Year_Plan_status_(since_2014)
http://jsoccer.com/new/jfl
In theory there's no reason why the NRL couldn't create a similar system. The criteria for membership of the professional tiers might be a bit different, but it could be done, and frankly I think Australian RL would be much better off for it in the long run. Unfortunately nobody in the RL establishment would ever accept such a system even if it could be conclusively proven that it's better for the health of the sport and league.