BCS officials have said they have tweaked this system as much as it will be tweaked, and are happy with it. The solution is really simple: WIN EVERY GAME, AND (unless you are Utah, Boise State, or Ball State for example) YOU WILL BE THE UNDISPUTED NATIONAL CHAMPION. Oh, Ball State lost to a Buffalo team? Forget Ball State then.
When great teams like Florida, USC, Oklahoma, Penn State, Georgia, Alabama, and especially Texas (insert PUKE) ALL lose a game along the way, this is the mess we get. The Sooners and Gators are playing the best of all these teams right now, and have survived the wars to get where we are now. You all might not like it, but it's just the way it is.
Heck, just put the 2 undefeated teams in the National Championship then and everyone can just shut the H*** UP!