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Let's see
>make the story linear and short, get that shit out of the way quickly
>since the games have to be about the legendaries anyway the main story is the professor asking the player to catch the legendary
>Rival is also searching for the legendary (gets the other version one before you)
>Evil team just want the legend for the money, so no world ending plot this time
>Gym battles equivalent now work as mini battle facilities, so all pokemon are the same level (or less), you enter with the full team and select the pokemon beforehand like multiplayer battles
>BP in battle facilities is now granted on how you did in battles (switching on NFE moves and doing SE damage, etc) instead of streaks
>the nursery now works as a menu, similar to the pokepelago, you put 2 pokemon directly from the PC into it and have the egg appear automatically over there
>you can now either take the egg with you or leave it in the nursery until it hatches (hatching works the same either way)
>you can now upgrade the nursery so it can handle more pokemon, eggs, and use items o change egg natures and stuff
>after the story ends the game really opens up, new areas open up everywhere with super strong trainers that you can re-match
>Add some cool indirect multiplayer thin like the friend safari