I cannot comment yet on how this has affected college options, but my D20 switched from a STEM charter to a local public school. While the STEM school was probably a “better” school in regards to core classes, she has encountered many more opportunities at the local public school, especially when it comes to electives, clubs, and athletics. You have to pick the best school for the child with the knowledge you have at the time. If your son wants to make the move (my daughter was the one who instigated her move), then he already has a level of intrinsic motivation.
I’m glad to hear he is switching. Your post resonated, since I was just like your son in 1980. At least in my experience, having my parents show that bit of trust in me and my judgments mattered a whole lot. I hadn’t told them so when I was begging to move schools and seeing the therapist they made me see, but I had already made plans to vanish a bit after the holiday break, thus forcing the issue.
Good luck to your son in his new school. He will see things there he likes and that he doesn’t like, but on the stuff that matters, he will be better off.