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It doesn't matter how ridiculous or Farfetched it is. I'll start:
Vs. Seeker
DexNav or equivalent feature
Ball Seals
Custom Pokeballs
Change Pokeballs
Black/white register menu
Following/Riding Pokémon
Properly done overworld encounters
Pokemon World Tournament
Better ai with refined movesets, switching/held items
Gym Leaders and E4 using strategy over simple monotype teams
Safari zone
Contests
Battle Frontier
Game Corner
Underground
Pokélathon
Photomode/Snap Mode (can turn in pics for money, items etc.)
Poke Pelago but expanded, something like Pokemon Ranch or a Digimon farm.
Bigger more challenging dungeons w/puzzles and secret items, hidden paths etc.
