BYU and with the overall softness of the program:

Marriage.

Coaches including conditioning coaches have only limited access to athletes outside the formal practice structure. But in order to be very successful, athletes must drive themselves and put in a lot of extra time in the offseason and outside of team practices. 18-21 year old, single athletes living in an athletic dorm with other athletes have a much easier time focusing on their sports, conditioning in the off season, spending extra time in the gym and watching game films and studying playbooks than their 21-25 year-old, married, sometimes with one or two small children BYU athlete counterparts.
Not every BYU athlete is in this situation, but there are enough of them to achieve critical mass. Now the Type-A guys like Austin Collie who also have very supportive wives are going to get it done no matter what, but other guys will have a hard time overcoming the friction young married life presents. I don't want to lump every woman into this characterization, but young wives typically want to be the center of their husband's world and want to absorb every last second of his free time. After a few years, they figure out the ugly reality that is most of us, but it can be very absorbing to be in a newlywed relationship. On top of that, while the wife of a professional athlete can see money coming in, the wife of an impoverished scholarship athlete with scant pro prospects will have a difficult time understanding why he needs to spend time outside practice on football. Those of you who frequently need to work late for no additional compensation know what I'm talking about.
While I have no insider's knowledge of the situation, I'm pretty sure married life and the demands of a new wife hit Jake Heaps up the side of the head like a 2x4. How else do you explain how a guy who's lived and breathed football his whole life shows up utterly unprepared the first season after getting married?
It's also a proven fact that married men have lower levels of testosterone than unmarried men. It appears to be a biological mechanism which prevents testosterone fueled aggression from becoming a danger to one's own offspring.