Any solution for the championship has to have the keep the following aspects sacred and yes, I do mean sacred:
1. Rivalries - Any solution that makes rivalries less important immediately is ruled out. "But rivalries will always be important, right?" Wrong! Look at Ohio State-Michigan. People bash the Big Ten now, but that single game has had probably the biggest impact on the national championship of any rivalry ever. If all of a sudden, both teams were still going to the playoffs and this only determined seeding, this game could not possibly be as important.
2. Conference Championships - Winning a conference is an age old tradition and has always been rewarded throughout the history of the sport. Teams that don't win their conference have never won a national championship (not counting independents). Teams who don't win their conference have only recently been given shots at national titles and all have ended disastrously for the entire system.
3. The regular season is a playoff - The playoff cannot trump the importance of getting there. If all of a sudden, you start just taking more teams, you are only going to make those regular season games less important. When a team can lose twice or three times and still have a shot at the title (without major help from teams losing), that only tarnishes the regular season's importance.
Like I said, a very simply solution to me is a 6 team playoff made of the top 6 conference champions in the BCS Rankings. This keeps rivalries as being important, makes it so winning your conference is a neccesity for winning the championship, and losing late could knock you out of contention. Not only that, but the limited amount of teams accepted makes it so that the regular season remains important.
To me, anything more than 6 (4 is ideal to me) just hurts college football.