Well...
1. I'd hire a competent writer who knew what an actual narrative and character development looked like. Failing that, I'd remove the narrative aspect out of Pokemon completely. It's got to be one or the other, because the current standard is so far below everything else that it's a joke. The games can work as either a story-driven experience or a player-driven experience, but not this half-arsed recycled approach each and every single time. I am absolutely fed up with Gen III's narrative.
2. Bring back everything that has ever been removed. Everything. It's time the games started making actual progress, not taking one step forward and two steps back as new features are added and old features are arbitrarily removed for no good reason. This, in my opinion, is the biggest problem with the Pokemon series: game mechanics are treated as gimmicks. It has never made any sense to take these things out. Mega Evolution, Z-Moves, the National Pokedex, following Pokemon, even the rubbish minigames like Pokemon Contests. All of these things should be in EVERY game, benefiting from the QoL improvements that are added to the core UI and battle system. Expansion is a key aspect to progression. Everything is coming back.
3. Expand the development team. Masuda needs to get it through his thick skull that for a game of Pokemon's size, you cannot work in a tiny team and expect to get a proper job done within the deadlines that he is working in. Fuck his preferences, frankly. The man is a composer, not a developer, and it really shows the way he has strangled the franchise over the years. It's time for that to change. A AAA-sized team and budget to reflect the fact that Pokemon is the highest grossing media franchise in the world.
4. Return the online functionality to Gen VI's PSS. Gen VII and VIII have absolutely garbage online features. The PSS was simple and easy to use.
5. This one would probably prove unpopular, but...I'd scrap the two versions model. One version, with postgame launch support in the form of free updates and paid DLC content. Free updates would be things like Mystery Gifts and challenges like new trainers and game rules, DLC content would be of a substance at least equal to the Delta Episode - basically, things you generally find in the sequels/third versions/alternates of a game. It's profitable but extremely anti-consumer to keep releasing 2 versions of an identical title, and I think in the long run it'd generate more player goodwill and more sales if there was just a single game that had 2-3 years of post launch support. "DLC" is an ugly acronym in the industry these days but it doesn't have to be: there is a lot of good DLC. Hyrule Warriors really got the balance right between free updates and paid DLC, and I'd want that kind of thing for Pokemon. If they REALLY feel the need to rake in more sales, then they can add a Game of the Year edition...or release a new region expansion similar to MHW's Iceborne expansion.
6. Add more in-game options. The choice between classic 2D sprites and 3D models, orchestrated and 8-bit music, the option to speed up animations, etc. Impossible? Dragon Quest XI S did all of that. No reason Pokemon can't either.
7. Oh, and whilst I'm at it...hire someone to do something about those old battle animations. Or multiple someones.
8. Add some support for older fans. Challenge Mode from B2W2 was a good start, but I'd want fully customisable difficulty: let people choose whether they want to turn on/off basically everything. Don't want to be able to heal outside of Pokemon Centers? Turn it off! Pokemon that faint stay fainted? Tick the box in the menu! Gym Leaders with higher levels and held items? Up to you! EXP share, yay or nay? Your choice! Players are quite capable of making their own entertainment here so I wouldn't want to go overboard, but but BUT it's not difficult to add options, and player choice is never a bad thing.
9. MULTIPLE SAVE FILES.
...that's about it. For the moment. I'm sure I'll think of more. Pokemon is so far behind the times and of such a low quality that it'd probably need a lot more to bring it up to standard.