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Give us skippable cutscenes. The Rotom Pokedex took a step in the right direction by being an always visible map with markers for where you need to go next in the story. You shouldn't need to sit down through a five minute cutscene mashing A when you could be playing the game. Especially when so many of these cutscenes have these bullshit "choices" that don't mean or change anything of value.
Overhaul some Pokemon stats so they can actually be useful. I'd go the radical route and say that all fully-evolved Pokemon should have a BST no lower than 500. And expand the movepools for Pokemon who struggle to accomplish goddamn nearly anything (but to a reasonable degree, obviously).
Give us an option to change the nature of shininess of a Pokemon. You could always set some arbitrary limit, once per save file, or it's really expensive, or a 24 hour turnaround time, whatever. Just as long as the option is THERE. Catching a legendary, finding out its nature is garbage, and having to redo the fight until you get a good one isn't fun. USUM at least gave us the Ditto Five thing, which was a great first step in helping players get competitive Pokemon faster.
Make every Pokemon catchable in some form in one game, including legendaries and mythicals. Locking Pokemon behind events isn't engaging or exciting, it's just exhausting.
Let us change the Pokeball our Pokemon is in after we catch them. Arbitrary limit: you can only change it once.
