First off I would do away with the BCS myself. I would have a playoff system where 8 smaller bowls would go into the Big Four bowls having 4 teams left for the final 4. The other bowls left out would be use as some sort of an NIT type for the teams not doing as good. Now as for the BCS this is how I would change it. 1. Downsize the 1A teams to the BCS Conferences and call it division 1. Another Division would be created for the Non BCS Conferences Where they would have there own playoff and call it division 1A. This way strenght of schedule would not come into play as much. 2. With the independents such as Notre Dame and others force them to join a conference having all conferences playing Championship Games. 3. Only Conference Champions would be eligble for the Championship game. 4. From there the BCS Formula could be used. Where only the clear number 1 and 2 in both polls and the computer polls were the same. If there is no similarity in all three polls, If two of the three polls agree then they would be used. If all three polls do not agree than the coaches of confereces, of the teams who are not involved would vote for the teams which would go to the National Championship game. Now this is my opionion do you have one.
