The best way to realign, if that's really the push, would be to organize 8 "super conferences" of 16 teams each based mainly on geography. That's 96 teams, and each conference would have an 8 team division. You'd have no cross conference play. Each conference would produce a single winner which would go to an 8-team playoff (random seeding). The rest of the teams would go to bowls against cross conference opponents.
That'd be the simplest, cleanest way to break things up, but I highly doubt it would go that way any time soon.
I also don't like the idea of reducing athletic scholarship opportunities for kids at schools 97-116 or whatever it is now.