Competition. Lark's 2 starts were against New Mexico State and San Diego State. He threw very well against New Mexico State, but they were one of the worst FBS teams that year. He didn't do nearly as well against SDSU in the Poinsettia Bowl, and the only reason we won that game was because of KVN going nuts on defense. Nelson started games against teams like Notre Dame, Boise State, TCU, Oregon State, Georgia Tech, and more. But even given that, their stats were pretty similar:

Lark: Efficiency 134.10, 61% completion, 6.7 yards/attempt, 8 TDs, 3 INTs
Nelson: Efficiency 131.40, 58% completion, 7.2 yards/attempt, 35 TDs, 21 INTs

http://byucougars.com/athlete/m-football/james-lark
http://byucougars.com/athlete/m-football/riley-nelson