Your going to get as many opinions as responses, but the only one that matters is your son's coach. If you think the Coach developing him on JV is going to be an issue then I'd like to suggest your son schedule a meeting with the Coach, and I'd like to hear how that goes. I can tell you how it would have gone with my 3 son's high school coaches....not too well. I don't know anything about your son other than you claim he is a five-tool player at 14 years old. I'm not going to comment on that claim because I've never seen a 14 year old dominate with all 5 skills against 17 & 18 year old
If I was the Head Coach and I thought he could bring value (wins!) to my Varsity program as a freshmen then I would play him somewhere (OF, DH, whatever) to give him at-bats or swipe a couple bases. So, this leads me to believe the following:
-Your son will get more reps at JV. Possibly the Coach wants to see him play before making a decision on moving him up. This is what I would do if I was the Coach...I would want to see him dominate JV games before moving him up to Varsity. Over the years and 3 high school playing sons, I've seen a lot of guys who are really good at practice and BP. However, when it was "showtime" they struggled because the game was too fast and they could not adapt to hitting breaking pitches. We live in a baseball talent hotbed. Many of the guys who make it to the next level play JV in 8th and 9th grade then get moved up to Varsity. A couple played Varsity in 9th grade but were used very sparingly, and they did not like it.
-Your son is not at the skill level of the 2 MIFS, but he is also not at the hitting skill level as the rest of the starters otherwise he'd be playing another position. Golden rule of baseball - Those that hit best, play. Therefore the Coach is giving him JV reps in the field and at the plate.
-You're going to hear the word "opportunity" a lot in the coming years especially if he is an aspiring college player. JV baseball is his opportunity to show that he belongs in Varsity. My advice is to take that opportunity and run with it. Force the Coach to make some tough decisions. Play Varsity outfield if it gets him to where he belongs as a starting point.
Good luck!