Honestly, unless the anime really surprised me, and I mean really surprises me, I think the structure of Goh's story is fairly locked in.
I see Goh eventually getting his hands on a Master Ball, possibly as a gift from Oak or Sakuragi, for all that his captures have contributed to Pokémon research. Then, after Ash has his big battle with Leon, Goh will meet with Mew. Naturally, Mew is not the kind of Pokémon Goh can just catch casually, so at that point, it's battle time.
How will the battle play out? Depends. If Goh meets Mew while just out there in the wild, maybe in the same place he saw Mew as a kid, Goh will use whatever six Pokémon you could call his "best" or "signature" team at that point, whatever it might be. If Mew decides to be more direct and meet Goh in the lab, Goh could have all of his Pokémon at his disposal at once. Either way, it'll be the culmination of Goh's character. All of his growth, all of his bonds, all of the lessons. The Trainers he's met, the Pokémon he's caught, everything Ash has taught him. It's all built up to this battle.
But Goh will not catch Mew. Even if Goh uses the Master Ball, Mew will destroy it with an attack. But despite failing to catch Mew, Goh will see that the bond of friendship he's forged with Mew through their battle alone is more powerful than any bond they could have forged through a capture. He's met Mew, battled Mew, and been acknowledged as Mew's friend. That's all he needs. And if there are any Pokémon Goh hasn't caught yet, let that pull double duty as a justification for why he doesn't catch the rest.
Ash has whatever experience is going to send him to the Gen 9 region. Maybe Paul is back with a Gen 9 Pokémon and kicks Ash's butt in a battle with it like Gary and Electivire did so long ago now. Goh is going to be contacted by his friend, Tokio. Being reminded that Tokio is looking for Celebi, the Johto boy has a lead on Celebi's location, and would like Goh to come to Johto to help him pursue it. Goh agrees to go to Johto for this reason. Koharu asks to go with Goh as well, having completed her character arc of developing from "normal girl that has no clue of her future" to "Pokémon girl that definitely knows her path" during this as well.
After a heartfelt and maybe tearful goodbye, this fellowship is broken as the characters go their separate ways.
I'm sorry, but Goh being a stand-in for new Pokémon GO players doesn't change anything. Trading Goh out isn't as big of a deal as changing Ash out would be. It would be like rotating out the PokéGirls over the years. Keep one tether for old fans with Ash, but trade out everyone else for the new fans. And in Japan, fans aren't exactly happy with Goh's character at all, so that's all the more reason to believe that Goh's time in the anime is limited.