Here's my entry! Geography is the name of the game. My favorite alignment structure is 8 conferences of 16, each with 4 divisions of 4. Nice symmetry, allows for 2-round conference playoffs if desired, and each school can play every conference mate at least twice in a 4-year period with a 9-game conference schedule. FBS retains its two de facto tiers (here the P4 and G4).
ACC
East: Duke, NC State, North Carolina, Wake Forest
North: Maryland, Virginia, Virginia Tech, West Virginia
South: Florida, Florida State, Miami-FL, South Florida
West: Clemson, Georgia, Georgia Tech, South Carolina
Big 16
East: Penn State, Pittsburgh, Rutgers, Syracuse
North: Michigan, Michigan State, Notre Dame, Ohio State
South: Illinois, Indiana, Northwestern, Purdue
West: Iowa, Iowa State, Minnesota, Wisconsin
Pac-16
East: TCU, Texas, Texas A&M, Texas Tech
North: Oregon, Oregon State, Washington, Washington State
South: Arizona, Arizona State, Colorado, Utah
West: California, Stanford, UCLA, USC
SEC
East: Kentucky, Louisville, Tennessee, Vanderbilt
North: Kansas, Kansas State, Missouri, Nebraska
South: Alabama, Auburn, Mississippi State, Ole Miss
West: Arkansas, LSU, Oklahoma, Oklahoma State
CUSA
East: East Carolina, Navy, Old Dominion, Temple
North: Army, Boston College, Connecticut, Massachusetts
South: Central Florida, Coastal Carolina, FAU, FIU
West: Appalachian State, Charlotte, Georgia Southern, Georgia State
MAC
East: Akron, Buffalo, Kent State, Youngstown State
North: Bowling Green, Central Michigan, Toledo, Western Michigan
South: Cincinnati, Marshall, Miami-OH, Ohio
West: Ball State, Middle Tennessee, Northern Illinois, Western Kentucky
MWC
East: Air Force, BYU, Colorado State, Wyoming
North: Boise State, Nevada, UNLV, Utah State
South: New Mexico, New Mexico State, Tulsa, UTEP
West: Fresno State, Hawaii, San Diego State, San Jose State
Sun Belt
East: Memphis, South Alabama, Troy, UAB
North: Arkansas State, Baylor, North Texas, SMU
South: Louisiana Tech, Louisiana-Lafayette, Southern Miss, Tulane
West: Houston, Rice, Texas State, UTSA
Here's a map for the P4:
https://imgur.com/qXPHTdN
And a map for the G4:
https://imgur.com/NYUS7B1
Unlike the 4 distinct divisions of each of the P4 conferences, the 4-team pods in each of the G4 conferences alternate between two 8-team divisions biennially (WAC-16 style). The P4 conferences each have 2-round playoffs to determine their champion. The 3 highest-ranked P4 champs are automatically eligible for the CFP. Each of the G4 conferences elect to hold a single CCG. The 4 champs of the G4 conferences face off in a 2-round G4 playoff, the winner of which plays the lowest-ranked P4 champ to determine the 4th spot in the CFP. Thus all FBS schools have a route to the CFP, although it's of course a lot harder for the G4 schools. Here's what a combined playoff bracket might look like (which conferences end up where will vary):
https://imgur.com/nGBnv2k
Some notes:
* As for why USF in the P4 and not UCF, it's "6 of 1, half a dozen of the other" to me. I just needed one extra Florida team to fill out the ACC South.
* The Army-Navy game is played earlier in the season when it's a scheduled conference game.
* Florida and Georgia play an OOC game in years when they're not scheduled in conference. When they do play in conference, Georgia plays OOC against Auburn.
* Alabama alternates OOC games against LSU and Tennessee, depending on which they play in conference in a particular year.
Notable annual interconference matchups: Air Force/Army, Air Force/Navy, BYU/Utah, Central Florida/South Florida, Colorado/Colorado State, Notre Dame/USC, Oklahoma/Texas, Pittsburgh/West Virginia, SMU/TCU