Missions can potentially be very useful to complete, and many of the rewards can be quite good. The highest priority available mission for each category (admin, diplo, and military) will appear on your mission list, with lower priority ones filling in if there are none in in category. The priorities and multipliers are given in the mission files in the mission subdirectory under the main EU4 game directory.
However, if there are multiple possible provinces or countries available for a mission target with the same priority, it can somewhat of a mystery which one the game will use for the mission. I present this list of the game's logic, based on my experience.
"Remove X from the map!": Target OPM will be the one you have a truce with, or alternatively the one that is allied to a small country on the other side of the continent that you can't get to, so the resulting war will take five years for no good reason.
"Colonize province X": If your dip tech is level 1, the province will be one you can't colonize because it's not adjacent to one of your provinces. Otherwise the one that requires the longest travel time.
"Turn X into a city": The ungarrisoned one with natives, if any. The mission will trigger severe, repeated attacks of native pyromania. Otherwise, the colony farthest from completing.
"Vassalize X": Target will be a country that can migrate, which will stop you from annexing it, or that you won't quite be able to ever get to 190 relations.
"Incorporate X into your country": Target will be the one the requires the longest wait before you can start to annex, or that will give you a new border you don't want.
"Increase relations with X": Target will be a country for whom the relations target is unachievable due to religion/border friction. Alternatively, the country that will rival you the month before the mission would have completed.
"Form alliance with X": Target will be the country you can't ally with because your country hates them. Alternatively it will be the country who hates you because their alliance offer to you auto-declined three days before you could take the mission.
"Attack X while they are weak": Target country will be France. No, they aren't actually weak.
I hope other players will find this of use.
However, if there are multiple possible provinces or countries available for a mission target with the same priority, it can somewhat of a mystery which one the game will use for the mission. I present this list of the game's logic, based on my experience.
"Remove X from the map!": Target OPM will be the one you have a truce with, or alternatively the one that is allied to a small country on the other side of the continent that you can't get to, so the resulting war will take five years for no good reason.
"Colonize province X": If your dip tech is level 1, the province will be one you can't colonize because it's not adjacent to one of your provinces. Otherwise the one that requires the longest travel time.
"Turn X into a city": The ungarrisoned one with natives, if any. The mission will trigger severe, repeated attacks of native pyromania. Otherwise, the colony farthest from completing.
"Vassalize X": Target will be a country that can migrate, which will stop you from annexing it, or that you won't quite be able to ever get to 190 relations.
"Incorporate X into your country": Target will be the one the requires the longest wait before you can start to annex, or that will give you a new border you don't want.
"Increase relations with X": Target will be a country for whom the relations target is unachievable due to religion/border friction. Alternatively, the country that will rival you the month before the mission would have completed.
"Form alliance with X": Target will be the country you can't ally with because your country hates them. Alternatively it will be the country who hates you because their alliance offer to you auto-declined three days before you could take the mission.
"Attack X while they are weak": Target country will be France. No, they aren't actually weak.
I hope other players will find this of use.