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ok here's some changes I would make, not to fix everything, but some things.
>after a team has been kicked out of a gym, there is a fifteen second window where nobody on the team kicked out can put a pokemon in.
>evolutions of mons give more candies. e.g. catching a pidgeotto gives 6 candies instead of 4, catching a pidgeot gives 10 candies. gives much more incentive to catch evolved pokemon
>fully evolved pokemon would give 2 candies per their set km with the buddy system instead of 1. e.g. Zard would give 2 candies/3km
>incense works on actual nearby pokemon instead of spawning new ones. works like weak magnets- if there's two-three people using incense walking together, it pulls slightly harder. if there are two opposing incenses, it winds up in the middle.
>menu to automatically swap x for y item from pokestops if your bag is full. for example, if your bag is full, you could set it to drop a berry for every ultra ball you get, to make room for and accept the ultra balls
>add an optional egg interface on the overworld, next to the buddy pokemon icon, with a progress bar for each egg. you can toggle which ones you want to display.
>completely remove the weird arbitrary cp scale. make it so that for any level, your maximum cp pokemon can be whatever you want it to be
>introduce a random possibility of powering up a pokemon 2 stages with stardust, ie powering it up twice with one payment of dust. just a rare bonus.