If it's the team that is the best, then you end up crowning a champion at the end of the season a la 1984. The ultimate version of this is the NCAA Tournament - high-level entertainment, but upsets happen all over the place, and the best team often gets bumped out.
I'd love to see the CFP expand for exactly this reason. I don't care that Clemson wasn't the best team in FBS this year. It was awesome watching them take the trophy from Alabama.