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Quite a few things
>putting stamina but not showing people any sort of stamina gauge leaving you to guesstimate if the gauge is full or not
>pokeballs can fail for no reason whatsoever and aggro wild mons
>while we're at it the entire fucking aggro system should be reworked
>some research tasks will turn someone away from wanting to use the pokemon (use a move on the mon you just caught 70 times)
>not enough pokeball varieties and they're not clear on the catch rates or the Feather and Heavy Balls other than Heavy Balls which should've been renamed to something else to avoid confusion
>you can't disable the final quest marker so you're stuck with a stupid circle following you around until you beat the shit out of arceus
>and on the topic of quests you can't have multiple quest markers active you have to manually go in and see which quests you can do in each area
>outbreaks can just abruptly end or change
>adding an inventory limit with the option to purchase more spare but then make money grinding tedious and then can only upgrade item space one upgrade at a time