JuCo > high school, no doubt. But Riley Nelson had a lot more experience this year than Cain had last year. Granted, Riley went down while Cain started most of the year, but this BYU season was already worse than Utah's last year before Riley got hurt.
Remember, Utah's only loss before the TCU game was at Oregon (who won the Pac 10 and finished ranked #11) by 7 points with a chance to tie or win at the end. Utah also barely lost at BYU (who finished ranked #12) by 3 points in OT. They weren't getting blown out by Air Force (beat them last year- when they finished the season in the also receiving votes category, where they will likely finish this season- assuming they still get votes this year after losing to Utah and TCU).
So Utah had less experience at QB coming into last season, plus had devastating injuries at key positions, and still did much better than BYU is doing this year (Utah finished last season ranked #18).
I don't think there is any question about it- Terrence Cain is/was/will be much better than Riley Nelson. And Jordan Wynn is/was better than Heaps so far.