Smith sees possibilities there, and even if looks bad now, it can be reborn. That’s what we’ve seen over the course of the series with the motel, what was initially deserted has become a home. Barry has taken the place where the worst moment of his life happened and turned it into something wonderful, the center of these peoples’ world. But, the darkness is still there, his fear manifested in the gray man sitting at the bar. Ultimately, we always have to deal with the bad stuff, but we must go on anyway. He may not see Shaun at the bar, but when he goes back in, he’s there.
All this would lead me to believe next episode will end with John bringing everyone together one more time, then disappearing for the foreseeable future. The episodes are called “His Visit” and it would make sense for the season to end when his visit does. If the series were to continue, we could jump ahead in time to the moment when he next returns. That would fit wonderfully with the themes, John’s goal was to show the characters what they could be, to be the catalyst for the halo effect, and then disappear when he is no longer needed, like the voices in the clinic. We see this literally in the speech sequence, where he gives us a brief glimpse of the Yosts in family portrait, happy for once. It’s still a long journey to get there, but it is possible.
So, keeping those two themes in mind, I’d argue that the central remaining issues are the rehabilitation of Cissy, and the reunion of the family. Cissy has a deep wound from her abuse of Butchie, and she’s completely unable to open herself up to him emotionally for fear of going back to that place. She deliberately keeps him distant, and yet keeps making comments that recall the moment. Here, she referenced him fucking himself, and has made similar references on other occasions. Subconsciously, she wants to apologize to him, but she can’t even find the words. Just going there would be too raw.
The same is true with Mitch, at first she doesn’t want him to help because she’s more interested in vilifying him than letting him make things up to her. It’s a surprise when he asks her what he can do to help, and ultimately he does wind up making things better. The Chemist also gives Cissy a reminder of who she once was, and who she could be again. He serves as a similar function as John, these characters don’t need people to act for them, they just need the prompting to act themselves.