Big 10 and SEC don't like that BIGXII get the championship and try to break away to 2 superconferences. Utah convinces the PAC12 to join them in a lawsuit. Legislators get involved and 4 divisions are formed. No one likes Utah and PAC, so they are left out.
During all of that BYU basketball also wins a national championship, losing only one game during the regular season.
Jesus comes back. BYU is declared the official school of the millennium. All other schools become BYU satellite campuses. All sports are intramural. BYU-tuscaloosa and BYU-Eugene show promise in football and may give BYU (because...remember the official school needs no identifier) a run for their money some seasons.
On the spot where Utah used to stand, there is an enormous water treatment plant built to service the entire Wasatch front. It's the only way to cover the scorch marks.
Referees actually call PIs and holds appropriately. Also, referee is a new priesthood office that includes ministration of angels. The sky cam shots are incredible. And they replay every call. They're fair every time, but it doesn't slow the game down.