1) All conferences limit themselves to eleven games per season.
2) All conference with ten or twelve teams have a 12th game conference championship game.
3) Seed six conference champions plus two at-large teams into an eight-team two-tier playoff with seven bowl games becoming playoff games.
This would be a longer-term project. For the 2008-2010 seasons, go to a Plus One format matching BCS #1 vs #4 and #2 vs #3, then a final championship game.
Your system sounds reasonable for the longer term. The top 4 BCS right now, however, would include #4 Georgia, and they are in second place in the SEC East. (I think the poll voters are giving the SEC credit they won’t afford to the Pac-10.)