I'm a generally positive D3 parent. But I would be the first to say that there's a lot of variability, both within a team, and between teams. I think that it comes down to what your son wants from a college baseball experience. There are D3 players who really do want to put baseball first, even though it's "only" D3, and there are D3 players who view it as a way to get a good education and keep doing what they love. Read this:
https://community.hsbaseballwe...caltech-beats-cal-lu
Is a team where players didn't start for the HS varsity "bad"? Is a losing team "bad"? Or maybe it's the team with 50 players that's "bad"? It all depends on what your expectations are. Plenty of us support D3 baseball and can explain why (see JCG, above).
My son's HS team is really bad this year. As in, painful to watch. Does that mean that playing baseball is a bad experience? It probably is for some. Can you be on a "bad" team but have a good experience?
I know many unhappy players, at all college levels. Does that mean the programs are all "bad" in some way? Would some of these players have benefited from knowing what they might expect going in (leaving aside that no-one expected a pandemic)?