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Ugh, well here's one I don't see mentioned often.
Battles in pokemon games. I think, excluding the double battle emphasis in Pokemon Emerald, it's just a constant bore-fest of single pokemon battles.
Why. Why? WHY.
Pokemon battles are the main thing in pokemon games, and yet Gamefreak haven't made any effort to diversify them or make them interesting. Take SM for example - single battles are the norm in most places. (let's ignore 3DS lag for a moment)
Why aren't there more options?
>double battles
>triple battles
>rotation battles
>battles where field effects are already in play (terrains, hazards, weather, Trick Room, etc)
>inverse battles
>limited/no item battles
>3v3 anime-style battles (i.e. not being allowed to plough through using 6v3)
>sky battles (bite me, bitches, at least it was new)
>type-specific battles
>in game Little Cup type events/tournaments
Can you imagine how interesting and diverse games could be?
You want to battle the Fighting Dojo? "Prove your skill with your strongest Fighting-type pokemon!"
You want to battle Olivia? Stealth Rocks are already on the field before you begin.
You want to battle Marlon? Permanent rain is falling on the field!
You want to fight Cress/Chili/Cilan? Triple battle only or no badge.
You enter Morty's Gym? Inverse battles are the norm.
It's such a small thing - it requires barely any work. And yet not knowing what types of battles lie on the next route would add so much diversity and fun to the game.