I've has some of these in mind for years while others are being developed as I'm typing this, but I'd basically want to expend on the mainline games in various ways by giving the player more ways to make progress in more than just the one direction that we're all familiar with.
There can be a type of trainer class system used, instead or more or less being forced too be a jack-of-all-trades type of trainer (aka the Ace Trainer class with your protagonist always being a glorified version of), expending on the core games' class system would allow for more role playing. I mean, you'd still have to have a mixed team for the sake of getting though certain routes, completing quests, and PVP, But, to play as a GYM trainer for example, you have to choose the "life path" of a sorts by capturing and training Pokemon of a certain type, and use that type against other players (either as PVP or PVE) in order to level up your affinity with that faction. Same sentiments for being a member of Team Rocket. So, in addition to being able to complete a campaign in the usual way of beating the Elite Four and Champion as a normal trainer, being a league staff member or a Team Rocker admin can have different stories to them, like having to either take over or liberate Silph Co. depending on the faction you choose.
Other not-as-important classes like Bug Catcher, Rocker and Hex Maniac can act as titles you can switch to and slightly increase stats and XP gains of Pokemon the correspond to the title in terms of type: like picking the Bug Catcher title will allow the bug Pokemon you use being up to 10% more resistant towards their weakness, Dragon Tamers can level their dragons 5% faster, Ace Trainers can earn 15% more money from NPC battles and selling items, and Breeders can egg hatching times divided by but to 50%. But for the sake of balance, title switching would have to cost in-game money, can't be changed for a day in real life to avoid the potential abuse in PVP, and, of course, only one active title per character.
As much as I'd want to see all of the regions in all of the games to be under a single roof, having a maximum of four would be more manageable; either combining Kanto, Johto, Hoenn and a Battle Tower region to start off with for example, or build a new region that can support at least three starting locations and have some variety in challenging and joining a few different factions, like going to Hoenn after finishing your "main story" in Kanto and defeating Team Magma as a member of Team Rocket. I'd also want to include some sort of New Game+ system after completing each region as either a league champion, GYM leader or high-ranking criminal by giving the option to have the NPC battles scale to your original region's collection and have things like your character level, money, inventory (especially TMs), titles, outfits and unlocked HMs (of which I prefer the Sun and Moon approach) carry over, or start anew with a new collection of Mons but with most things still carrying over.
And as for some other things that don't need a dedicated paragraph:
Obedience from Pokemon gotten though trading with actual people should be determined by your character's level. Player homes similar to Fallout 76's C.A.M.P. system. Maybe take a look at competitive Pokemon and include around 300 of the more notable Mons from the various tier lists since including all 898 wouldn't be worth it. Have the wild Pokemon appear on the field. Have the game look in the same perspective as Sword and Shield but have it look as good as Let's Go Pikachu and Eevee. Limit the player count to no more than 16 people per server, but a higher limit for Battle Tower/tournaments. In-game tournaments mimic competitive Pokemon's tier lists by having filters and restrictions for ubers, overuse, underuse, every thing goes, and so on, which each playing being able to specify which tier they'd like to battle in. Pacifist mode/repels for NPC trainers and human players. Co-op. And still battle the legendary and mythical Mons during their respective story events, but don't let them be catchable outside of mid to high character level weekly events. And no Master Balls.
@camitalo: I mean, sure. It's all "easier said than done" and different people have different way on fantasizing about it either based on what they feel is lacking from the core games or pulling things from MMOs. But I think the point here is less about actually collaborating and designing a game, and more about just making brain go brrrr by basically writing fan fiction.
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