You're on the right track. The only thing that makes logical sense would be a complete reorganization of college football into something like you propose. I've always thought that 8 10-team regional conferences with promotion/relegation to 1-AA makes a ton of sense.
The problem is that it will never happen. Money is the big reason, but there's a whole lot of practicalities that make it impossible. Reorganization and realignment will continue to happen, but as it has already - in fits and starts, piecemeal, and unequally. That means deciding a champion will always have some fuckery to it.
We used to argue about who is #1. Then the BCS came along and we argued about the top 2. Then the playoff and we argued about the top 4. Now it's top 12(ish). If they expand to 16, I guarantee that #17's fans will be pissed off in the first year. We as Texas fans are mad right now, and probably rightly so, but there's diminishing returns on the number of teams you put in the playoffs. The 16th best team doesn't actually have much of a chance to win it all. Honestly I kind of doubt that the 12th best does. Fourth best might.
The one change that intrigues me a little bit it just getting rid of the committee. Use a computer, or Elo, or whatever and just be done with it. Publish the parameters that go into the calculation. At least that way everyone knows what they need to do.