The six BCS conferences would each be required to have a conference championship game, the winner of which would represent that conference in the playoffs. Only conference champs are elligible. None of this at-large bid crap. You don't win your conference, you have no business even being able to think about the possibility of a national championship.
Then, the midmajor conferences would play out their regular seasons as usual, but would not have conference championship games. Instead, a ranking system similar to how the BCS works now, would determine the top 4 conference champions from among all the midmajor conference regular season champions. In lieu of a conference championship game, these 4 top midmajor regular season conference champs would play in two \"play-in games\" with opponents based on seeding according to the same formula that chose these 4 teams in the first place. These two play-in games would happen at the same time the major BCS conferences are having their championship games, and would determine the two teams that will represent the midmajor conferences in the playoffs.
Once that's settled, we'd have the first round, which would be:
SEC Champion vs ACC Champion
Big 10 Champion vs Big East Champion
Pac 10 Champion vs Big 12 Champion
Midmajor Play-in Game 1 winner vs Midmajor Play-in Game 2 winner (to placate the mid-major conferences for being second class citizens in the world of D1 college football, the winner of this game would receive the official title: NCAA Division 1 Midmajor Conference College Football National Champion, so the little schools would always have something to play for)
Notice that the first round is not based on seeding. The same conferences always play each other no matter what their ranking is. The purpose of this is to help set the stage for a quality national championship game that is truely national in scope. It is designed to eliminate regional matchups from the national title game, so that you will never see something like Auburn vs Clemson or Pittsburgh vs Penn State for the title.
Round 2 would be the round 1 winners playing each other in something I imagine would be marketed like the fianl 4, but this time it would use seedings rather than regional considerations, so conferences wouldn't be locked at this point. So then you'd have (just as one possibility:
SEC/ACC champ vs Big East/Big10
Pac10/Big12 champ vs Midmajor \"national champion\"
The championship game would, of course, be the winners of these two games playing each other.
Several points I like about this system:
1.) No independents. Sorry Notre Dame. No join conference, no play for national championship
2.) Because you must win your conference to get into the playoffs, the importance of the regular season and the conference title are not diminished. Every game still means something, just as it does now. None of this \"nothing ekse matters as long as we make the big dance\" attitude like in basketball
3.)Elimination of the possibility of regional matchups means the title game will always have national interest in separate areas of the country.
4.) The mid major conferences are sufficiently placated. Mid major conferences are given lots of incentives to do good and improve their programs. They would have their own title game built into the playoffs for bragging rights amongst themselves, and 1 mid-major is always guaranteed a trip to the \"final four.\"
In short, this system assures that the national championship is decided ON THE FIELD, while preserving the integrity of the regular season and the conference championship, it treats small conferences fairly, and it keeps Notre Dame out.