From the Idaho Statesman:
"After redshirting at Boise State in 2014 following one season at Butte (Calif.) College, Stuart appeared in nine games in 2015, attempting 18 passes (one touchdown) and rushing 30 times, scoring three touchdowns. He only played in three games this past season, completing 3-of-5 passes for 50 yards and rushing once for 2 yards."
Tommy Stuart was more than capable of being the starting QB at Boise State. According to the MountainWestConnection.com:
"Harsin has good reason to like the state of his quarterback position. Whereas most teams fear their starting quarterback being taken away due to injury, the Broncos appear to have good depth after Friday's showing against the Bengals. Both Stuart and Rypien operated under a sense of calm and poise, never seeming to be in a state of duress. Stuart brings a dual threat in his ability to both throw and run the ball. Rypien on the other hand has a big and accurate arm. This combination of talent should provide for an intriguing offensive showing."
in the end, the Broncos' coaches went with Rypien and his prototypical arm instead of Stuart's dual-threat capabilities and leadership skills.