An eight-team playoff of the top ranked CONFERENCE CHAMPIONS would be my solution. What the BCS is right now would choose the eight teams and seed them. The first round played at the higher seeds' home field and the next two rounds in the rotation of major bowls. If done according to Saturday's BCS poll:
#8 seed Michigan (Big 11 Champ) at #1 seed USC (Pac 10 Champ).
#7 seed Virginia Tech (ACC Champ) at #2 seed Oklahoma (Big 12 Champ)
#6 seed Louisville (C-USA Champ) at #3 seed Auburn (SEC Champ)
#5 seed Boise St. (WAC Champ) at #4 seed Utah (MWC Champ).
Notre Dame would be treated as a conference unto themselves. Now you've eliminated every excuse. You must win your conference title to go to the tournament. You must be one of the top eight conference champions according to the BCS standings to go to the tournament. No conference gets an automatic berth. Every conference champion has to earn their way in (big and small alike). There are no "at large" berths so there is no decision making to be done. From there, it's strictly brackets.