I thought that myself when I read that article that talked about a Data Scientist(tm)
My idea is that there should be an eight team playoff at the end of the season. The winner of every BCS conference gets a spot in the playoff. If there are conference co-champions, such as this year in the Big Ten, the team with the higher BCS rating gets the bid (this year it would be Penn State). The two remaining spots are at-large bids, reserved for schools from non-BCS conferences or independents (so Notre Dame won't cry). These spots are decided by BCS rating (the two highest rated non-BCS-conference teams who win their conference or independents) get the bid. If there aren't any ranked non-BCS-conference teams who win their conference, a selection panel gets to decide which team gets into the playoff.
Also, no conference can have more than one team represent that conference in the playoff. The teams are seated by BCS rank (the highest BCS ranked team would play the lowest BCS ranked team). The teams that do not make it to the championship game get distributed to various bowls. These bowls do not have to be BCS bowls (BCS bowls do not have to be forced to select #19 Virginia Tech).
The regular season would have to be pushed ahead at least one week. That means Championship Saturday would fall on November 29 this year, round 1 would fall on December 6, and round 2 would fall on December 13. The championship game would be played about a week after the bowl games (no change from when it's played now).
Since the majority of games are played against conference foes, the regular season will stay important and the bowl system will still be preserved. And think about the non-conference matchups we would see, since teams aren't as afraid to lose out of conference because the main priority is winning the conference championship to get that playoff spot. Also, the stereotype of which conference is best or worst can be done away with. Because every conference has its shot, we will know at the end of the playoff how strong conferences and teams really were.
This year's playoff teams would look something like this (based on BCS rank):
1. Oklahoma (Big-12)
2. Florida (SEC)
5. USC (Pac-10)
6. Utah (Mountain-West) [at-large]
8. Penn State (Big Ten)
9. Boise State (WAC) [at-large]
12. Cincinnati (Big East)
19. Virginia Tech (ACC)
The match ups would be:
1. Oklahoma (Big-12) vs. 19. Virginia Tech (ACC)
2. Florida (SEC) vs. 12. Cincinnati (Big East)
5. USC (Pac-10) vs. 9. Boise State (WAC) [at-large]
6. Utah (Mountain-West) [at-large] vs. 8. Penn State (Big Ten)
The only problem I see with this system is having to wait awhile before finding out who goes to bowl games. A season running this late would probably be hell for the bowl selection process. If Penn State makes it to round 2 of the playoffs, we would have to wait until December 13 to find out if they are going to the Rose Bowl or if Ohio State is going to the Rose Bowl.
What do you think?