The solution I'd like to see would retain the current ranking system, but rather than just taking the top two teams it would take the top 4. #1 playing #4, #2 playing #3 (or #1 playing #3, not sure yet) and the two winning teams would then play each other for the National Title.
It would mean more games so the schools get more money and it would end any possibility of there being dual champions; no one could female dog that one team was screwed. Every game would still count because you have to excel to be in that top 4, but it would give teams like Auburn the chance to actually fight for the title instead of being screwed over like they were a few years ago. There would be a single undisputed winner at the end of it all and the two losing teams could fight it out for third in one of the other bowl games. You could have the 3rd place game played in the last year's Championship stadium and you could keep the current bowls. They’d have to alter the schedule a little bit, just subtract a single week from the off period, but I think it could work out very well. Hell you could kick off the bowl season by playing the two playoff games and then finish it with the championship.
Granted it could lead to #1 being beaten by #4, but that’s part of the excitement.