You're never going to know the best team for sure in any year. It's the nature of a one and done format. That being saidany system employed should include at least the conference champion, as determined by the conferences themselves, of all eligible conferences. That means at least 5 teams. In order to give the competition some semblance of fairness (as opposed to only money), it should be an 8-12 team tournament (The more the better but I don't think 16 gives enough advantage to the top seeds).
Take a look at the history of the NCAA Basketball Tournament. During the UCLA dynasty, USC could actually lay claim to being the second best team in the country. However they never got a bid because they never won the PAC-#. As the field got bigger the tournament got better, which brings me to point #2. More teams = diverse field = better product. Refer back to the basketball tourney. There has only been one year (maybe two, but I think it's only one) since the tournament began seeding schools where all four of the top seeds made the Final 4. The best team is not always the national champs. Take Duke/Mercer from last year for instance. Duke probably wins that game 9 out of 10 times, but for whatever reason, they didn't bring its A game. Duke probably had a shot at the Final 4, but a Champion does not look past an inferior opponent.
12 teams (or even 10) in football allows room for the for the 5 5CSMA champions, more access for the non-5CSMA and two or three wild cards. Of course there will be arguments regarding bubble teams or that a 2-loss SEC team is better than a 1 Loss ECU, but that should 1) be proven on the field and 2) If the 5CSMA really are better than their redheaded step brethren, ECU won't advance in the tournament, as I envision it.
Here is my plan for a fair playoff. Poke holes 'til your hearts' content (P.S. I know it's a pipe dream).
First off, 11 game regular season schedule. Not 12.
Field: 12 teams
Contenders: 5 CSMA champions 3-4 highest ranked Non-CSMA, 3-4 Wild Card
Format: Single elimination.
Particulars:
-Top 4 teams get a 1st round bye. (If 10 teams then two play-in games between 7-10 and 8-9...and THAT'S WHAT THEY ARE CALLED).
-First round will be played on a 5/12, 6/11, 7/10, 8/9 basis at the home field of the lower seed.
-Teams are reseeded after each round. So if a 12 seed happens to beat a 5, they play the 1, not the 4 seed.
-Top two seeds before any round do not meet before the NCG.
-Second Round will be played at the field of lower seed.
-Third Round = 2 of 6 New Years Day Bowls.
-Final = NC Game one week later.
Who, besides the 5CSMA, is against this?