Region 1 could include the Big 10, Big East, Notre Dame, Navy, Army, and other northeast based independents.
Region 2 could include the ACC, SEC, Sun Belt.
Region 3 could include the Big 12, C-USA, WAC
Region 4 could include the Pac 10, Mountain West
You would eliminate all conference championship games ( I know this would be a dealbreaker) and instead conferences would have their teams play a heavier conference schedule. For example, You might play an 10 game SEC schedule instead of an 8 game schedule. All conference champions are in the playoffs, and there are 6 teams per region. If that happened, this is what it would look like. 1st and 2nd seeded teams get byes.
Region 1- 1. Cincinnatti, 2. Ohio State, 3. Iowa, 4. Penn State, 5. Pittsburg, 6. Wisconsin
Region 2- 1. Alabama, 2. Florida, 3. Georgia Tech, 4. LSU, 5. Miami, 6. Troy
Region 3- 1. Texas, 2. Boise State, 3. OK State, 4. Nebraska, 5. East Carolina, 6. Missouri
Region 4- 1. TCU, 2. Oregon, 3. Oregon State, 4. USC, 5. BYU, 6. Utah.
Now I know this would never work, but you could play out the seeds, then give them a break to let them have the regional finals in bowls and play it out from there. I would just like to see teams like Boise and TCU get a shot to see if they belong. Heck, I'd like to see Cincy get a shot because I really think in a one game scenario they could give Texas fits, and maybe Bama.