I'd would drop the BCS system. It seems like the Media and Coaches have less room for error than some arbitrary statistical formula. The ACC, Big 12, Big 10 (11), Pac 10, and SEC champions would get automatically in one of the 4 big Bowls. The Big East would lose their auto bid because of the reduction in quality football teams in that conference.
The two best teams from the six non-automatic conferences would have a championship game. That winner would get into the field of 8 teams. There would be two at-large bids available for the two highest ranked teams (average of the coaches and media) that did not get an automatic bid. There would be a list of tiebreakers or a formula used ONLY in the event that the poll average was the same for two teams.
There would be no limitations on how many teams came from a particular conference. If a conference has 3 of the top 8 teams in the country, they all deserve to go.
The teams would be seeded 1-8 by a committee like the NCAA tournament has. This would help avoid nightmares like the Florida/Miami Orange Bowl we had last year. The four bowls would be round 1. The next week, two of the four bowls would get round 2 games. The Championship Game would go to one of the two bowls that didn't have a round 2 game.
Oh I forgot one thing. Teams would be limited to 11 regular season games unless they were playing a non-conference game against Hawaii (really the only way Hawaii can get teams to play against them). You could still have the early (preseason) games but they would count as one of the 11. If you put a cap on the regular season, it helps countbalance the impact of two additional games for the two teams that play in the Championship Game.