My daughter had this happen. Before her mission, she was running cross country for a community college in Arizona, before giving up the sport. Right when we moved to Utah, The church lowered the age for sisters to 19, and she decided to go on a mission. She had a high GPA in high school and had two semesters of college with good grades as well (from her time in Arizona) but still got rejected. My sister-in-law had connections to the admissions department, and we got feedback as to why she was turned down, despite having good grades even in her two semesters of college. In short, BYU Play stay low value on the community college she went to in Arizona. Long story short,

Long story short, she was advised to enroll at LDSBC (now called Ensign College) and if she could get good grades there, she would almost certainly get in. She did that for one semester and reapplied, and got in. She since has graduated from BYU.

I don't know if this is the path that your son can take, but that My daughter had to take, but she eventually got into BYU.

Funny. I wrote all this and then realized that I'm blocked by crimedog. So whatever.