BYU just doesn't have playcallers with any balls on both offense and defense. That's 100% the issue. And even worse, their head coach is a pretty good defensive playcaller but he runs away from that duty at every chance he gets.
I think one of the problems for college teams is that when they look around for assistant coaches that they seem to believe that they need to find the guy in the NFL or in high level college somewhere. You want Mike Leach, you don't want Mike Leach's O-Line coach that has no experience calling plays running your offense. Yet teams do that. And if you can't get those high level guys, go find some guy that is killing it in high school that understands that offense can be played beyond a 10 yard box or that blitzes and press coverage are not things to be avoided, and that actually knows how to call football games instead of promoting schmucks from within that haven't called plays before.