A change is as good as a rest

Make PMD focus more on the characters involved and not on the story as a whole; it would make it not only more interesting to play and not that straightforward, but also let us get to know individual characters more and discover their personalities, strengths, fears, etc. (Well that's for me, I feel like that is only thing missing in PMD)

 

I could go for changing (or rather making a side series of) Pokémon to be sort of an action-adventuring game. Imagine this: somewhat-open-world kind of like Zelda, except it's you the human and your Pokémon allies who are traveling the land saving people and fixing their problems. You have your six Pokémon, one of whom at a time is following you and is AI controlled. Or you control one of your six ready Pokémon at a time (swapping on the fly when you want) while the human is following you AI and just doing the human things, or you control your human while in towns. And just because it's now action based with actual fighting doesn't mean there's killing! Just replace "faint" with "run off into the brush or dig into the sand or get withdrawn by the trainer" and it still fits perfectly well.

Here I am, playing as a Typhlosion, with Fire Punch set to X Button and Rollout set to Y Button, exp grinding against a bunch of Weepinbells and my trainer is following behind me on foot, maybe commenting on how the Weepinbells climb back into the trees once they're slain defeated. Oh no, what's this, I need to cross a stream and there are a bunch of Gravelers on the other side? Let me just hit a button and switch out for Quagsire for a bit to adapt to traversing the environment and the anticipated open-world enemies up ahead, like changing my equipped spell in Elder Scrolls while my almost-useless follower trainer human does nothing but carry the narrative.