I think those two types of coop are going to make things very difficult for players. Basically, if you’re playing with 4 people, and two of them want to work together, and the other two just want to go do their own thing, then they can’t. All my friends who I play Minecraft with play differently. Two of them are always teaming up to do huge builds, while the rest of them are pretty independent.
I really think that if each player controls a group of their own citizens then the gameplay won’t be affected much at all. They can take their citizens halfway across the world and start building houses, or they can contribute to the town right there with their friends. The only issues I can see with it might be things like food supplies and other resources. But if all resources are going to be stored similarly to how wood is stored on the stockpiles, then there could easily be a lock button implemented. Click the stockpile and lock or unlock it. Unlocking it would make it freely available to any other players, and locking it would make it a private stockpile that only you can contribute to, or pull from. Only the original creator of the stockpile can lock or unlock it.
I think that would completely simplify the coop and keep everyone happy.
ADDITION: I suppose that there could be some pretty heavy treachery going on with the lock feature. Because civs seem to drop supplies off at the nearest stockpile (I mean, who wouldn’t? Ain’t nobody got time for that.) there’s always that chance that you’ll be mining or woodcutting or farming, etc., dropping your supplies into your buddies stockpile, then when it comes time to use those resources for crafting or building, BAM! He’s locked it on you and now you feel betrayed and sad.
However… You might just write Radiant a letter, thanking them for filtering out your true friends for you.