OP already admitted that what his son did is what's best for the team. OP and his son are not happy bec what is best for the team is not what made his son shine. To me, the question isn't what he should do to correct this "injustice". The question to me is why the OP puts a higher importance in his son "shining" and moving up the lineup over and above doing what's best for the team. Why not encourage his son and tell him he did what he is supposed to do and be very happy with that, and be happy with his role in the team whether it be batting in the 10th position or being on the bench. If his son works hard at practice and has the right attitude, it will pay off sooner or later. And if didn't pay off, then it's still an amazing life lesson that would carry on to whatever he does in life.
I can imagine that this attitude of what's best for me personally regardless of whether if it's what's best for the team (or the company I work for or the country I live in) is what's leading to all these problem we see in society.
I simply don't agree with you. JV baseball, a one year vacuum. Best for the team? To what end? Make the playoffs? There aren't any. Develop into a better player, YES. But, that requires playing time. The goal of EVERY kid is to play as much as possible. EVERY KID. Players need to make an impression on the coach based on that coaches criteria if they want to play.
Is swinging 3-1 at a pitch you don't love ideal, of course not. Could it be necessary, maybe.
The primary objective of the game of the team sport of baseball is to score more runs than the other team to win the game. Nowhere in the guidelines and rules of the game does it imply that a team should not try to win the game because there are no playoffs. Nowhere in the guidelines and rules does it stipulate that the objective of the game changes because it is "JV".
The objective of the batter is to make his way around the base path to score a run and/or help other teammates score a run(s). There are multiple ways of doing so. Nowhere in the guidelines and rules of the game does it imply that a batter should do something different than the objective in order to impress the coach.
When learning team sports properly, players will understand that their primary individual goals should be to help the team win the game in whatever role they are filling at that time. Yes, it should also be the objective of the individual player to aspire to contribute as much as possible to the team goals. Earning increased opportunities comes from skill development in practice (and other avenues) and execution in games. This is earned over time and, yes, often it is necessary to re-earn it day in and day out (wait 'til he gets to college!).
A successful team must have a sufficient number of players to handle injury, situational needs, etc., so not all will be starters. A successful HS program must have more than sufficient number of players considering inevitable funneling of players to other interests, eligibility, injury, extent of development or lack thereof, etc., and therefore is likely to carry even more players than necessary at the sub-varsity levels. So, even more so, not all will be starters. This, too, is earned over time and often it is necessary to re-earn it day in and day out for a wide variety of reasons, including a new coach that may not yet be dialed into each players' skill set.
There are many ways to earn and re-earn. What you are suggesting could, potentially, be one short term way. But it is certainly not the right way with the right approach to the team sport that is baseball as defined by the game itself.