This is also why I fully expect to see the "Big 5" football conferences leave the NCAA in 12 years. I think this playoff system is a trial run (especially if they go though with their threats to all play 8 conference games and only play OOC games against each other) to see if they can be profitable on their own. Then when they leave the NCAA, they will pay athletes and it will essentially become a minor leagues for the NFL.
I think you're right. The NCAA will either be pushed aside or there will, at least, be sweeping changes. Everyone is sick of the NCAA.