I think it would be awesome if Niantic added in-game cooperative quests to add some depth to the game, and encourage more cooperation.
For example, at a random time, you will get a notification saying "[Gym name here] was taken over by Team Rocket!", then you could go to that gym, and battle the AI placed team rocket pokemon, and after you succeed, a cutscene will start, showing Giovanni announcing that he is taking over your local area! Oh no! You will then unlock more missions(and harder ones), involving going to certain gyms, visiting specific locations/pokestops, and uncovering secrets. You will have to work together with players from other teams to defeat Team Rocket once and for all! They could do so much with this. They could have massive Boss Fights, similar to raids, where players work together to fight Giovanni and the team rocket executives, and they could even release legendaries in this way! You would earn exclusive items from these quests, including evolution items, coins, and XP. They could also update this system with each generation (Team galactic, plasma, etc.). What are your thoughts on this idea? (not like it will ever happen!)