Some of this advantage was a product of a fairly soft schedule: Southern Utah, Idaho, Texas State, UNLV, Colorado State and New Mexico State. But the Aggies beat Louisiana Tech in Ruston, they hammered San Jose State, and lost to Wisconsin and BYU by 5 combined points; Utah State was a couple plays from playing with the big boys, not Toledo, in their bowl game.
Utah State is a tough team to get a solid read on because of the level of competition they faced. Chuckie Keeton is 17th nationally in EPA, but drops 49 points and 23 spots in the rankings when we adjust for schedule. Kerwynn Williams drops 21 points from 88.2 to 67.2 when we adjust for schedule, and is 69th among running backs in EPA+/pass (although his production from catching passes survived schedule adjustment). In almost every category, Utah State drops from near-elite based on performance on the field, to good but not special when adjusted for the quality of the competition they faced. In 2011, Utah State was rated as a having a legitimate, elite ground game.
My second point of concern is that Utah State in 2012 had the nation's best red zone defense. They allowed 3.0 points per possession (e.g., a field goal on average). The second best was Notre Dame at 3.3 points. They were the only team that allowed touchdowns on fewer than 30% of possessions, and were even 2nd in turnovers on downs in the red zone. The problem here is that red zone defense isn't really a unique skill. Certain qualities may help a team be good in the red zone - strong against the run, allow a low completion percentage - but outside of these qualities, there's no reason to believe that a team can repeat strong red zone defense from season to season. Utah State should regress in this area in 2012. If they were drop to a respectable 20th (which is still better than their EP3+), that would cost them .3 points/possession, and would drop them from 3rd to 13th in points/possession allowed. That would cost them a game or two in 2013.
Finally, they lost Gary Andersen. I don't pretend to have any special insight, but anyone that could make Utah State competition in football at a national level is unique.