Maybe let only the host control time. I think most people would play coop with a friend, so it wouldn't be a problem to coordinate this with the other player. Or you let both players control time and it changes for both. If the other player doesn't move during that time on map he just waits. If one player is in a battle, either the game pauses for the other, or it continues normal and the battle is displayed for him on the map until the other player finishes it. It really isn't a big problem to figure these things out and coop would definitely be a lot of fun.