I think the solution is to simply have the top four teams in a playoff, I think it will solve 90% of all of the problems, adding more rounds, will not have a good enough marginal return to justify it, because more rounds will make injuries more of a factor as to who wins the title.
That wouldn't help the undefeated minor conference teams though who couldn't crack the top four (AP) before bowl season:
2009 (6) Boise State 13-0
2008 (7) Utah, (9) Boise State 12-0
2007 (11) Hawaii 12-0
2006 (9) Boise State 12-0
2004 (5) Utah 11-0, (10) Boise State 11-0
Maybe, to offset injuries, you can cut one non-conference regular season game from everyone.