Two years ago, Oregon was largely written off after quarterback Jeremiah Masoli was dismissed from the program after one too many run-ins with the law.
Now, Thomas can declare for the draft and no one blinks an eye. The redshirt junior is the reason why.
He stepped in for Masoli in 2010 and took Oregon to an undefeated regular season and berth in the BCS championship game, throwing for 30 touchdowns against nine interceptions.
And Thomas had nowhere near the game experience Bryan Bennett will take into spring practice as the expected starter, something the lanky Texan did not get as Masoli got the boot in June.
Bennett, a redshirt sophomore from Encino (Calif.) Crespi, saw significant action against Arizona State after Thomas hurt his knee. Starting the next week at Colorado, he threw for 156 yards and two touchdowns and rushed for another 69 yards on six carries, creating a bit of a controversy in the process.
Regarded as the best dual-threat option Oregon has had at the position since Dennis Dixon, Bennett is a more natural passer than Masoli and better runner than Thomas. His presence will make the zone-read and triple option that much more dangerous as opposing defenses are forced to account for him.
Bennett is the future of the position, whether or not he was actually set to challenge Thomas for the starting job this spring.
Oregon will be fine over the long term, as Kelly has built one of the most quarterback-friendly offenses in college football. Since taking over as offensive coordinator in 2007, his signal-callers have thrown for 132 touchdowns against 45 interceptions.
In the last two years, that ratio jumps to an absurd 80-16.
Bennett, or whoever takes the snaps for the Ducks, will put up huge numbers.
The concern will come with the extreme lack of experience behind Bennett. The only other scholarship quarterback currently on the roster is freshman Marcus Mariota, who redshirted this year.
If Bennett goes down, Oregon is in trouble. Think back to 2007, when a dream season fell apart after Dixon tore his ACL. Think back to 2008, using three quarterbacks against Boise State after Masoli was concussed.
Kelly will have to work quickly to bring everyone up to speed, though a lightweight non-conference schedule of Arkansas State, Fresno State and Tennessee Tech should afford all four plenty of reps.
It is a major concern, but still not enough to dislodge Oregon as the favorite in the Pac-12 North, not with so many experienced players on both sides of the ball returning. But coupled with the loss of running back LaMichael James, it makes USC the unquestioned choice to win the conference and drops the Ducks out of the preseason top five.
Still, Kelly's remarkable track record means Oregon can't be counted out just yet.
Everyone is replaceable. Kelly takes that mantra to its extremes, and with great success.
Dan Greenspan is the publisher of Cal Sports Digest and covers the Pac-12 for Fox Sports/Scout.com. Follow him on Twitter @DanGreenspan.