Here's a concern you almost never hear:
Once you expand to the 16-team model, how long until you start getting Division I-A (aka FBS) flooded with smaller programs, all wanting a piece of the playoff pie? That's what's happened in basketball.
Up until about 2000 there were about 300 NCAA D-I basketball teams. Now there are 350. So in a decade, we've seen a 17% increase in the number of teams.
There is so much to gain from having a shot a making the show. If you can win your conference, crappy though it may be, even though you'll only get to the play-in game, you gain TV money and serious brand recognition and exposure for your school.
It will likely be the same in football. 11 conference champs? There are currently 124 teams in FBS. If there's a 17% increase, that's about an additional 21 teams. I can name you 15-20 teams that are borderline ready to move up right now.
That's 2 more conferences. So now it's 13 conference champs and only 3 at-large bids. How long until that's not enough and they decide to go to 32 teams?
Where does it end? In basketball, they recently considered expansion of the tournament to 96 teams. Fortunately, they decided against it, only expanding to 68. I still remember when it was 48 (and I'm young compared to those who remember it as a 16-team tournament).
I'm really in favor of the biggest programs breaking away from the NCAA and creating their own association of 80 or so teams in 5-8 reasonable (both size-wise, competition-wise, and geographically) divisions/conferences for all competition. Keep your championships to a reasonable size too and watch the TV dollars roll in.
I think you raise a great point with the 16-team playoff model. The more teams you let in, the greedier you see other schools get. And I said, you'll be seeing the #17, 18, etc, thinking they "deserved" it. Also, the rewards on fielding a competitive football team trump that of men's basketball, so I totally see where you are coming from.
The winning the crappy conferences doesn't just extend to the "small" conferences in basketball. As a Colorado alum, i'll be the first to admit in a "real" conference, we would have little chance at best being in the dance this past year. But because the Pac-12 was so weak and went on that run in the conference tournament, we got the program to heights thats have been seen in many years.
There is basically two *unofficial* classifications of 1-A/FBS schools, you got the "BCS" level ones and the "mid-majors."
I do think the current NCAA basketball works, although I do think they'll eventually expand to 96 and then fold the NIT like they've talked about before and making those first round loses play a consolation tournament (reminds me of youth tennis). I wouldn't mind if the NCAA went back to 48 teams, but that's not happening. Just keep it at 68 hopefully, makes the brackets fun.