At this point they should just create 4 conferences named SEC, SWC, MidWest, and WestCoast. Take the schools with the 64 highest athletic dept budgets, let them play and determine a conference championship and wild card, play an 8 team playoff (seeded by rankings of said top 8 teams) and declare a national championship. If you school can't sell tickets or compete financially you and the service academies can play in Div 1AA.
For basketball create eight 16 team conferences and do something similar.
For other sports, do what you want, nobody really cares that much.
Go ahead and tell me what is wrong with my idea, you can't because it is awesome.