Here comes a long post.
Great work! The presentation of your ideas were phenomenal. This is something a lot of fans would buy into, because it actually uses logic! Here is my feedback:
Pros:
1.) A fair playoff
2.) Regional ties, rivalries, etc.
3.) Constant competition, fighting for top 3 or avoiding bottom
4.) Abilities for achieving/underachieving schools to move up/down, every school has a chance to win title
5.) Opportunities for same big money sponsorship
6.) BCS sucks!
Cons:
1.) One bad year/coaching change/rebuilding, can land you in the cellar for potentially 5-10 years.
2.) Say Texas goes 5-7, and drop. Their fans are not going to be happy having to play in the 2nd league the following year and having a 0% chance of a championship.
3.) That kind of massive overhaul would need the agreement of 120 schools, impossible to suit everybody's needs
4.) Big $$ contracts will keep feeding into B10, PAC12, and SEC etc and those conferences won't dump those, even if they control a new group of teams.
5.)The SEC fans would be against it, because they wouldn't get their media shoe-in into a BCS championship.
6.) Everyone would schedule cupcake out of conference games to ensure staying in division. (this could be solved by forcing the #5 seed in east to play #5 in west etc)
I encourage you to spread this idea around, maybe more people will look at realignment with more logic and creativity.