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First of I want all of these features back (and in a single game):
>Following Pokémon
>Fun minigames with good rewards (e.g Pokéathlon)
>VS Seeker
>Battle Frontier
>Customizable player-owned home (e.g Secret Bases, the villa in Platinum)
>Trainer customization
>Black Tower/White Treehollow
>PSS
>DexNav
>SOS battles
>Horde battles
>Apricorn ball crafting
>Double grass
>Trainer Card score
>Hard mode
>Medals
>Join Avenue
>Hyper Training
>Poké Ride
>Safari Zone or Friend Safari
Second I want the narrative to be absolutely minimal and the world to be somewhat open. The player should decide their own pace and where they want to go next (within reason), and the story should be told via optional tidbits that you can pick up and piece together by talking to NPCs and reading books or journals. In other words, it should generally be modeled after Johto.
Third, I want much larger and longer dungeons in the games. Even the biggest and most complex dungeons in this series - Seafoam Islands or Mt. Coronet for instance - can still be conquered in a flash with just two Max repels. I'm talking Zelda kind of dungeons here - between 50 minutes to well over an hour long depending on your aptitude, assuming you go through it for the first time with no prior knowledge, and with plenty of puzzles and obstacles.
Lastly I want regular patches and updates to adjust the game balance along with transparancy by the developers in the form of videos or forum posts where they explain their thought process behind the changes and respond to feedback. Oh, and I also want there to be two regions.