The biggest downside for BYU is that I doubt they'll ever get whiff of a BCS Bowl as an independent. Had they stayed in the MWC, there's always that possibility of going undefeated, winning the conference title and getting the at-large bid. There was also a chance of gaining AQ status had they stayed in the MWC.
I just don't see them putting a schedule together that leads to an undefeated independent season that get's them ranked high enough at the end of the year.
BYU is going to have a higher profile, be seen on ESPN, get their local TV market back and make more $$$$, but they're also going to be farther away from the BCS then they've ever been. Does that get Cougar fans excited?