Who chooses the moves made for each city-state during redeployment? I assume the ultimate decision goes to the controlling faction but it's not spelled out in the rules.
Team decision and there is an overarching rule that says if you cannot sort out any situation, the controlling faction decides. In fact in the rules it states that when order becomes an issue the order is: Athenian Controlling, Spartan Controlling, Athenian opposition, Spartan opposition. This is why it is not repeatedly stated in every rule, its in the beginning of the rules.