With the current system we have now, the two best teams in nation should play for the championship regardless of what conference they belong to. The question that is the most critical and most subjective is "who" exactly are the two best teams in the nation.
LSU is number 1, no doubt. The controversy seems to be centered on who rightfully deserves the number 2 spot: Bama or OSU. As far as strength of schedule goes, Both AL and OSU played four ranked teams during the season. Alabama played two additional teams that were ranked at least once during the season to OSU's three. I've been playing around with some numbers. For each of the top three teams, I looked at their schedules up to this point. I gave a value of 26 to every non-ranked opponent at the time LSU, Bama or OSU played them and then summed up all of the games played based on rank. I then averaged out the sum by the number of games played and found that LSU had a schedule strength of 17.46, Alabama was 21.5 and OSU was 22.25. Coupled with OSU's one loss to an unranked Iowa State, I say Bama edges them out as the 2nd best team in the nation. This is just what I've been messing around with, the BCS has a much more comprehensive system which of course is what this debate is all about.
Here is a tournament system I thought of that also implemented the four main BCS bowls:
1) All NCAA division I FBS teams are divided into 8 national conferences. (For kicks, lets designate them the Big 12, Big ten, Pac 12, Mountain West, Atlantic Coast, Big East, Southeastern and Sunbelt conferences).
2) For the Western division, The Big 12 and Big ten conference champs play each other in the Rose Bowl; The Pac 12 and Mountain West conference champs play each other in the Fiesta Bowl. For the eastern division, The Atlantic Coast and Big East conference champs play in the Orange Bowl; The Southeastern and Sun Belt conference chaps play in the Sugar bowl.
3) The winners of the Rose Bowl and Fiesta Bowl play off for the Western division title at one of the two locations; The winners of the Orange Bowl and Sugar Bowl play off for the Eastern division title at one of the two locations.
4) The Western and Eastern Title winners meet to determine the national champion at one of the four locations.
The problem is all of the smaller bowl games. Everyone wants a slice of the earnings that they bring in so we cant get rid of them now.