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It's not as big an intrrusion as it sounds. I believe they have the right idea. All the details have yet to be worked out. But, there will be 2 bowls played to allow 4 teams a semi final. Then, the two winners will play in the plus one, or championship game. So, the intent is to continue to use bowl games to determine the final 2 teams, then they play in the plus one.
I think the idea is there will be 4 to 6 bowl games that 2 get picked for the semi final on a rotational thing, just as it is now with the BCS. The whole thing about a panel is to just be certain the top 4 teams make it in. You can't go with just 4 conference winners and always have the best 4 teams. Some conference winners may lose 2 or even 3 games. A two game loser who is winner of the MAC should not get into the round of four over a one game conferencee loser of the SEC, Big Ten or probably the Big 12, either.
So, the panel will likely chose 1 of the 4 teams. That choice may be a non conference champion but they will have criteria to meet to insure they get the right team. ie. strength of schedule, etc,