Actually just use the 11 conference champions, the top five BCS teams as wildcards, and seed in order of BCS rank.
I think you'll get a different outcome and some good regional matchups to boot.
Also, there would need to be a stipulation on stadium size--60k or more you're fine, but less than that, and the home team must either find another FBS or NFL stadium to play in, or forfeit home field advantage.
Otherwise, you won't get the bigger schools on board, lest they have to go on the road to play a Southern Miss or TCU (the later especially has piss-poor facilities, and still will after their ongoing renovations.)