Let's use 2010 as an example -- #1 Auburn 13-0 (SEC Champs) #2 Oregon 12-0 (Pac 12 Champs) #3 TCU 12-0 (Mountaint West Champs) #4 Stanford 11-1 Only loss was #2 Oregon by 21 points #5 Wisconsin 11-1 (Big 10 Champs) They beat Ohio St. Only loss was @ Mich State #6 Ohio State 11-1 #7 Oklahoma 11-2 (Big 12 Champions) In this scenario, there was a clear cut #1 and #2. But who would you take in spots #3 and #4? You would look at TCU's schedule and probably leave them out, in favor of Stanford and Wiskey.... but they beat Wiskey in the Rose Bowl 21-19.
It's not going to be fair. The ACC, SEC, Big 10 and Pac 12 all have conference championship games. Last year, FSU was undefeated. Ohio State was undefeated and played 1 loss Michigan State in Big 10 title game. Auburn was #3 and played #4 Mizzou. Michigan State won which eliminated OSU. The winner of Auburn and Mizzou was going to play FSU for the title, which was Auburn. This year will be no different.
The coaches in the Big 12 were never in favor of the Conference Championship game because they believed it hurt them. In some years, it has. But the SECCG has been REALLY good for our conference. Look how many years winning that game put someone in line to play for the Crystal?