The problem is that for all the conferences to agree to this they are going to want to have their share of the pie.
Looking at your situation from last year:
1. LSU
2. Okie St
3. Oregon
WC1: Bama
WC2: Stanford
WC3: Arkansas
That's three SEC teams while you you have Boise, Georgia(who actually played for the SEC Crown), Wisc, Va Tech, WVU, Clemson and the other pretty highly rated and pretty damn good conference champs(aside from Boise) left out for 3 SEC teams, two Pac 12 teams etc. There would be an absolute shit fit if three SEC teams ,made it in. Let alone two of them that didn't even appear in the conferences championship game. Whether we like it or not we have to view this from the prism of what would actually happen/be possible. I really doubt you're going to get the conferences to agree to a set up where one conference can put three teams into a BCS game and where a top 10 ranked conference champ is left out for two teams that didn't even win their own conferences division.