I think there should be a 16 team playoff. All eleven division 1a champions get an automatic bid and then the five highest ranked teams that are not a conference champion. Seed the teams and start the first week of December with the higher seeded team playing in their home stadium to guarantee a sell out for all games. Eight games week one, four games week two and two games week three. The school payout will depend on how far that schools team advances. Each win gets a bigger piece of the pie. Have the championship game on at 5pm EST on New Years day. Have it rotate with the traditional New Years day bowls. I think you would then have a true champion that would be hard to dispute their legitimacy.
I know some will argue that not all the D1 conference champions deserve to go but if they are designated as D1 and it is a D1 championship, they have every right. It might give a new perspective to conference realignment and where some of the more talented kids decide to go to school.
Just my thoughts