The spread option offense that has taken the Ducks to three straight conference championships and BCS bowls won't work in the professional ranks, they said.
And that's exactly why Kelly will be an NFL coach someday, to shut them up.
In a lot of ways, Kelly's demeanor is better suited for the next level. He doesn't seem like the kind who lives to be in a recruit's living room or glad-handing boosters. At Rose Bowl media day last month, Kelly looked like a condemned man strapped into an electric chair as he was bombarded by questions.
In the NFL, he can live in the film room when not on the practice field, free of backwards NCAA rules and regulations and job requirements. He can be a football coach, not a nanny, not an academic advisor, not a bureaucrat.
In the NFL, the focus is solely on Sunday. Right now, it's often anywhere but the game.
In the NFL, Kelly can focus solely on Xs and Os and scheming like the offensive mastermind he is.
And he would succeed there. If the Denver Broncos can install the zone-read and other option principles on a whim, what could Kelly do with an off-season to implement the real thing with personnel brought in especially to run it?
"It's a very good scheme," California defensive coordinator Clancy Pendergast said in December. "He does a great job with it and he is a very good teacher."
Pendergast, who served as defensive coordinator for the Arizona Cardinals during their run to the Super Bowl in 2008 and spent 15 years in the NFL, shot down the main concern about Kelly's offense, that it would expose the quarterback to too many hits.
"A lot of those runs that the quarterback makes on the perimeter, he's out in open space," Pendergast said.
"Now if you want to run him tackle to tackle, he's going to take more of a pounding. But when you get out on the perimeter and all you are asking a guy to do is carry it 3-7 times a game to keep the defense honest, then most of the time he's out there by yourself."
Consider that Carolina Panthers quarterback Cam Newton rushed 126 times as a rookie for 706 yards and a record 14 touchdowns, an average of 7.87 carries per game.
Thomas carried 7.15 times per game in 2010 and only 4.3 per game en route to Oregon's first Rose Bowl win since 1917 this past year.
Those totals include sacks, where the quarterback is more at risk, as Newton noted.
"If I'm running, I know this may sound kind of crazy, but I feel more comfortable with protecting myself rather than in the pocket and being defenseless," he told the Charlotte Observer last November.
Kelly has already proven his scheme works against Pendergast, Pete Carroll and Monte Kiffin in college. Against an LSU defense loaded with future pros, it was special teams turnovers that did in the Ducks.
If the zone-read doesn't work, Kelly is smart enough to adapt. He knows how to create mismatches. That won't change, even if his offense has to.
Kelly has to have thought about these things, or why even take the Bucs' call? Why begin contract negotiations?
And the interest will keep coming. Kelly's statement announcing his return is carefully phrased to not lock him in beyond this season.
Nowhere does it say his heart is in Eugene or he plans to be a Duck for life, just that he has "some unfinished business to complete at the University of Oregon." Maybe that means winning the BCS title or simply dealing with the forthcoming NCAA report regarding Will Lyles, but definitely doesn't preclude him from making the jump at a later date.
As everyone knows, there is nothing Kelly loves more than making someone shut up.
Dan Greenspan is the publisher of Cal Sports Digest and covers the Pac-12 for Fox Sports/Scout.com. Follow him on Twitter @DanGreenspan.