What I did not understand:
1) Not including the big, loved feature that was customization in ORAS. This was stated to be so people had a reason to continue buying XY, but it was still very disappointing not having it in the RS remakes. Glad they have stuck with customization otherwise.
2) Removing the button to always keep your running shoes toggled on after HGSS. It should have stayed in the games that came after it so I didn't need to keep holding B! Doesn't matter much for the recent games, but for older titles it was noticeable.
3) Fresh Water healing more HP than a man-made Potion invented specifically to heal HP.
4) Already mentioned, but the Game Corner should have been replaced with minigames rather than outright removed.
5) More relevant for modern games but - why say our Pokémon wishes to be petted while in battle, when we can't pet them!? This just makes no sense, especially when we could pet them during this prompt in 3DS games. They could definitely have added this in if they wanted to with the Switch's touchscreen.
Natures, EVs, and IVs. and Kanto.
How many RPGs let you distribute points freely when they are obtained?
Like the skill points in Fallout and Dragon Quest?
That's the kind of system that should replace EVs. When levelling up, grant EV points. When in the Pokemon menu, let the player distribute these EVs freely like it's Pokemon Showdown.
Or each game should intentionally include designated EV Grinding areas and give the EV-boosting Held Items and Consumables to the player ASAP if the opponents are going to bring out full teams of perfect-coverage perfect-nature perfect-IV perfect-EV monsters as soon as you hit the first Gym/Rival Battle.
Feeling like I agree with this as well lately. EV training makes sense from a 'spend more time playing our game' standpoint, but it still is exhaustingly long/boring and I would much rather speed up the grind. The real work and challenge comes from figuring out how to use Pokémon with high EVs on your teams, what moves to give them, etc and that challenge will always be there - but the EV training process to get to that point is honestly tiring.
Can't say I feel the same agreement towards replacing natures with styles though.. I feel like natures give Pokémon more personality, which has some importance in a game with hundreds of creatures to capture and raise vs Smash with much less. There is also less of a need to differentiate Smash characters since they already have set personalities from their own games, and in Smash itself each character can only be obtained once. I think natures make sense to keep personally, especially since the menu now states what stats they boost.