With the type of season that college football has had, it's hard to tell who exactly the "best" two teams were at the end of it all. I think the championship game pitted the two teams with the best records (as far as wins/losses, SOS, etc.) at the end of the regular season together.
Georgia was probably playing the best football out of everyone at the end of the season, but it's hard for me to think of them playing in the championship game when they didn't even get to their conference championship.
USC also had been playing well after overcoming a slew of injuries through the season, but anyone that loses to a 4-8 Stanford should not be in the title game IMO.
Missouri got screwed when it came to the BCS. Yes, they had two losses, but to the same team (OU). I think if they play anyone else in the Big 12 South during the season, they would only have one loss and be headed to a BCS game, but that's the way it goes.
There was no way that Illinois should have been in the Rose bowl. With three teams ahead of them in the BCS standings (2 non-Pac 10 teams), they should have been counting their blessings to even get to Pasadena. The Rose Bowl needs to recognize that their are more conferences than just the Big Ten and Pac 10.
Congrats to LSU and the other bowl game winners. Watch out for my WVU Mountaineers next season. With Heisman hopefuls White and Slaton, along with Noel Devine, we'll be a hard offense to stop. A new coaching staff will hopefully implement new schemes and we'll have a solid defense returning.