Both of this options are "first world problems" but I think the answer comes from what your RC tells your son about the weaknesses in his application and the kind of person he is.
If he has a strong academic background, the maturity to succeed with little guidance, and is ready to go to college, then ROTC is probably a better option.
If his in immature for his age and did not have the rigorous high school academic experience a year of prep school could help establish those foundations.
The other advantage of ROTC is the additional nomination and appointment opportunities. ROTC cadets get to compete for service connected nomination.