I don't understand why people care so much about a College football 'National Champion' in the first place.

College teams range from teams of legitimate students to school-affiliated minor-league ringers. Teams across the NCAA and even in individual conferences play radically different sets of opponents in a statistically insignificant number of games.

It's no wonder any kind of ranking or playoff system is going to be a mess; there's very little coherent data to base any of this on. It should be no surprise that computer rankings are unsatisfactory: garbage in, garbage out. The various 'expert' and coaches polls aren't any better, since they are depend as much on hot-air 'what-if' virtual games played out in the pundits minds than actual on-field games.

LMoE

Well, that's the whole point: implement a true playoff system. And it wouldn't be a mess; you just start with the conference champions.