I'm in a similar hypothetical dreamworld as Gattaca on this one - with some differences.
If they (NCAA) were smart, they would figure out the most important things for the schools to maximize revenue and reduce costs, while keeping important issues like AAU and research at the forefront. The easy way to do this is to strip football out of the equation. Leave the conferences as they are (or let them revert to more regionally based and academic initiative focused reasons), and have conferences for Olympic sports and academics. This should help in the cost of travel for low revenue sports and keep good rivalries in tact. Then make football its own, high $$$, t.v. based mega draw event.
Something like 4 - 18 team Superconferences (MidEast, South, Central, and West for example) geographically based with 2- nine team divisions seeded based on the prior year's results (with consistent tie-breaker rules from top to bottom). Each team plays 8 divisional regular season games, which leaves 4 self-scheduled games that can be used as rivalry games or whatever. This gives 72 teams with a shot at a 4 team playoff.
At the end of the regular season, all 72 teams play in a bowl game set up as 1 vs 1, 2 vs 2, 3 vs 3, . . ., 9 vs 9 of the divisions in the same conference. This would give balanced, and regional bowl games played in the area to attract crowds. The 1 vs 1 would be a playoff quarter final game and the 9 vs 9 would be a relegation game; while still having 36 bowl game + 3 playoff games.
The other 56ish teams would also be set up in 8 regional divisions and have the 8 winners compete in a play off where the top 4 teams get moved up to the P4 conferences the following year. There could be additional bowl games if necessary.
I love the idea of the super conferences being basically static with some changes and shifts, but the divisions constantly shuffling so there are always new and exciting match-ups by taking the results of the bowls to seed the following year's divisions (winner of 1-1; loser of 2-2; winner of 3-3; loser of 4-4; etc would make up a division).