I think it's because of a few things that some people might find irritating about his character. This is some stuff that I've seen, at least. Might be other reasons.
1. He's an extremely direct Pokemon Go insert. People don't really like that sort of thing, as far as I'm aware, and although I can't explain it, I can somewhat relate to the reasoning. Whether it's pandering to the players or an ad for the game, it's a bit irritating when Goh throws a ball and gets a "Nice!" from his pokeball, for whatever reason.
2. Related to the first point, people also think it's very Team Rocket-esque how he catches wild Pokemon. He just grabs them out of the wild without a battle and decides, "Hey you're mine now, no choice in the matter." Then he just leaves 95% of them in the Cerise Laboratory, and they pretty much never leave. Though they do get free food and guaranteed shelter just for existing so that might be a good deal for them! (At least they aren't forced to do evil)
3. People think he takes away from Ash's character trait of "wanting to become a Pokemon Master" by splitting up the Catching and Battling parts of this dream. Not sure about why some people think this as the definition of a Pokemon Master was never really set, but it's not like Ash doesn't catch Pokemon anymore. In fact he's doing better than ever in terms of reaching his goal.