blackbox, I factored in per team with the NFL numbers. Also, not saying SEC has been better throughout history, just moreso in recent years.
Conan, in 2007, it seemed nobody wanted to play for the National Championship. I said last year when USC lost and Florida lost (I think it was the same weekend) that neither team could complain if they get left out because they had very winnable games that they completely blew. Had USC played a conference championship game against the #1 team in the nation and won, and Florida didn't, guess who Oklahoma would have been facing.
2006 wasn't entirely different. The only undefeated team that was left out was Boise State and their schedule was a joke that year (see undefeated Hawaii and Tulane of years past). Utah is a different animal, but when you play in the MWC you have to do better than scheduling Weber State.
But the bottom line in this system is that you can take any 3 teams that cannot meet during the season in all of FBS football, and no more than 2 of them can be said to control their own destiny. To that extent, there's a flaw in the system, and it's no more the SEC's fault than it is the PAC 10's fault (or whatever other conference).