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Okay, so this is gonna be a long post filled with mostly shitty opinions, but here I go.
Something I hate about every main game is they always take away good features and/or replace them with something not even half as good as the original. For example, the PSS, Battle Frontier, Contests or Secret Bases. Also, they can do amazing stuff without a lot of effort which could add some spirit to the games, such as giving some Pokemon special animations, walking in the overworld or changing the battle music, or make a massive effort which would really worth it. So, a Pokemon game with every best feature from previous games AND adding some good shit would make the best Pokemon game ever.
I have a lot of ideas, most of them are shitty fangame level, but they could add them very nicely if they purpose to. (also, sorry for my bad English)
>Pokemon walk in the overworld
(extra points if they make it optional so bigger Pokemon don't mess with the screen)
>Gym battles can be in any order, they adjust to your current badges
(first 2 gyms have only 2 Pokemon in their 10s; next 2 have 3 in 20-30, next 2 have 4 in 40s and last 2 have 5 in their 50s, or something like that would work)
>Bring Contests / Super Contests back, if possible mix them with the Musical from BW so you can dress your Pokemon for extra points in the current category and make it not only dependant from the Poke Puffs or Poke Blocks.
Make Z-Moves and normal items usable in them, too, so they can add a lot of extra factors.