I was thinking the same way as your son. I did not want to go any other way; my goal is Marine Corps and I didn't apply for any other academies simply because I didn't see myself in any other branch.
I, too, fell short with my test scores. I believe it's the reason why I'm here at NAPS. Here are my credentials:
SAT: 1680 | Math: 520 | English: 590 | Writing: 570
ACT: 26 | Math: 24 | Science: 24 | English: 27 | Writing: 27
GPA: 4.0
Other NAPsters here share the same credentials as I do; some are here because they couldn't pass physically, or they couldn't get a nomination because their districts were incredibly competitive. All of us are here for some reason, and they decided to keep 250 of us so we got the chance to improve and go to USNA. I'll forever be grateful for this opportunity. If your son gets offered NAPS, don't take it negatively; if anything, it's better than going direct because your son will be prepared.
I love it here. Of course, there are the athletes that don't like it because it's too disciplined or too strict, but it's the military. It is strenuous and difficult to be far away from home, however for me, the amazing people I met here keep me going and I don't go one day without laughing or smiling. The academics are challenging too. The one thing I've learned so far from NAPS is to fail. I rarely let myself fail in high school, but it's because it was simple and I hadn't really been challenged academically before. But when I came here, I learned the hard way. I ended my first marking period with a 3.68 GPA though, and I'm very proud of it. NAPS is the best way to go.