Obviously these are my suggestions, and a lot of them are quite popular anyways:
Pokestop/Gym Submission. We’ve gotten vague hints at this recently in the latest few updated, but it is still arguably one of the most needed and requested features in this game. There’s at least 10 places locally for me that fit the whole Ingress portal criteria, but relying on another game shouldn’t be how the system works.
My idea is that every person is allowed to submit a specific number of stops a week depending on things like Trainer Level. Level 30-32 could submit 2 a week while Level 35-38 could submit 4 a week.
Some more immersion on rainy days. I know the point of the game is to get you outside but in the wonderful climate by me that’s not viable at least 1/2 the time. I would like to see some NPC storyline/battling, which could incorporate both the quest and PvP systems into it.
A more accurate way to find raids. The current raid locating system is awful. I’ve always been relying on 3rd party raid maps because the one in-game only shows you raids if they’re within 1/4 mile of you. It doesn’t work most of the time. If Niantic could either extend the raid map so you could see raids further away or just added a universal raid map of their own to the game it would fix a lot of problems IMO