How else could it be done? A true playoff has to include ALL 11 CONFERENCES. The BCS system is a crock, it doesn't give us a true Champion, it gives us a beauty contest winner.
You're preaching to the converted. It'd be nice someday to see a team handed a trophy that reads "NCAA DIVISION I FOOTBALL NATIONAL CHAMPIONS".
Like this:
Arrange the conferences so we have 16 conferences of 12 to 16 teams each (192-256 schools). Each conference has two divisions. The division champs play each other to determine conference champs. Only conference champs can progress on to the 16 team play off rounds. "Elite Eight" (four games) would be New years day.
Independents?
two choices:
1) They choose to be independent, so they do not participate in the play offs. Tough. Their decision
2) Have a "Independent league" (I know sounds contradictory), but, One slot would be reserved for the Independent that is either the highest rated or has the best record.