Hmm, this is a tough one; there's plenty of things big and small I'd like to shift around of this show, and the one I eventually landed on risks coming off somewhat loaded, so I hope my explanation will be satisfactory.

Specifically, if I could change one singular thing and only one, I'd probably make it so Ash is officially retired as a protagonist after XY, keeping everything the same before then. While I'm aware this can come off as 'haha SM/JN bad', that is not the intent at all.

Specifically, I believe with the benefit of hindsight, XY's ending really marks the transition between older and modern Anipoke; while DP's ending is also a major breaking moment, XY's ending led to the departure of several writers that had been with the series since the early days, and we know from interviews during MPM that Tomiyasu actively wanted to portray Ash differently than he used to be, ontop of the general structural and tonal shifts like decreased emphasis on action and a wackier style of humor. And from there on out, even with its differences, the following series have never quite been like the older ones.

Therefore, I find that SM and JN occupy an awkward spot where they're still technically connected to the past, but still feel quite different in ways that are often more harmful than beneficial. I feel for JN in particular, Ash's story arc and general writing is the weakest of the main trio, not really attempting to advance his character and with not great handling of his team, battles and plot points, keeping a lot of expected energy but feeling somewhat phoned in in execution. There's definitely quite a bit I could say on this topic, but in general, I think most of what I like of SM and JN comes from elements that aren't Ash.

I think HZ shows well that SM and JN could have benefitted from a different protagonist: Roy may fit an Ash-like niche, but being a new trainer means no one is up in arms when he loses a fight or when he's not acting in the way expected of him, avoiding situations like how the excellent debut episode for Project Mew was overshadowed by people disliking Infernape's handling and Ash's performance against Moltres. While this would also mean a lesser amount of continuity, I honestly believe that could actually improve JN given how several cameos and nods detracted from the story told more than they helped, and quite a few of them didn't actually require Ash's presence to be kept.

In general, I believe A different protagonist would free SM and JN from the constraints attached to following the past series, and allow them to be more of themselves. While I would probably be slightly dissatisfied by Ash never winning a League if his run ended in XY, I feel that's one change that would be to the show's benefit as a whole.