Lots of comments in the BCS post below about a playoff system. Here's my two cents:
I have yet to hear of a playoffs concept that actually works in a way to avoid controversy. A 4-team playoff is a complete joke and shows absolutely no insight by anyone who advocates it as a way to avoid controversy. If you think finding a 1-vs-2 is hard, try figuring out if the 2/3/4 teams are better than the 5/6/7/8 teams.
Similarly, an 8-team playoff is too few in a lot of ways: Either some conferences are excluded or some worthy "at large" teams are excluded. And picking the field is brutal: The difference between teams ranked 2-15 can negligible. You can usually make an argument that a team ranked in the high teens might be as good as the one ranked No. 8. Regardless: Significant controversy continues to exist. And isn't the goal of a playoff to eliminate controversy? If we're still going to have controversy, we might as well keep the existing system.
16-team playoffs begin to get there, but if you thought it was hard to distinguish the teams at the margin of a 4- or 8-team playoff, try arguing that No. 15 or No. 16 is decisively better than Nos. 17-25. Plus, I defy you to find an AD who will allot four weeks to play a playoff AFTER a full regular-season. Again: College football is going to have MORE scenarios like this season, not less. If eliminating controversy is the goal, then let's REALLY let the teams play it out on the field.
I still like my old idea, where the only people who get screwed are the ADs more concerned with money than with the game. It's very simple: Create a half-season-long playoff that lets everyone in and therefore produces the most meaningful, least controversial champion. It's unrealistic, but only because the powers-that-be lack the imagination to see its genius:
(1) Increase the number of D1-A programs from 119 to 128.
(2) Play 5 regular season games: Your annual "tradition" games, your homecoming, your cupcakes, whatever. This also allows teams to find their stride.
(3) National Bye Week. Rank all 128 teams, using the same committee system that fans have come to accept for college basketball. Except this committee is NCAA officials, media and a few computer gurus. Place into four 32-team regional brackets.
(4) Play Week 6. Number of playoff teams remaining afterward: 64. Losers are eliminated and have 24 hours to cut deals to play each other in Week 7.
(5) Each week, the bracket advances along. Winning teams move on to the next game on their bracket. Losing teams are eliminated and may cut deals to play any other eliminated team the following week, creating an innovative, musical-chairs-style free market of scheduling that will also keep fans engaged.
After Week 7, 32 teams are left. After Week 8, 16 teams are left. After Week 9, 8 teams are left. After Week 10, 4 teams are left. After Week 11, 2 teams are left. (Again, eliminated teams simply pick from the increasingly deep pool of eliminated teams to fill out their schedule.)
(6) Teams that are over .500 are eligible to be selected to play in the 25 different bowl games played in December and early January; bowls may invite any teams they want, again creating a vastly more efficient market than the current system where a team is slotted to a bowl by its conference finish.
(7) The final 2 teams play in the championship game.
The biggest problem is that schools can't finalize their teams' travel or ticket sales plans a year in advance, as they do now. If that's the biggest problem -- but in exchange fans get the best championship tournament in sports and an undisputed champion -- I think fans will take it.
Everyone in, controversy out.