I think it would be great if alliances could choose (by voting or something) what each of its members should prioritize, or what enemies said members should fight. If an alliance is at war with 2 factions, they should split up their forces and attack or gather in one huge zerg wave and overwhelm them one after the other. Maybe throw in some dynamic quests as well, where the alliance chooses between a set of objectives that they get certain rewards for doing? This system should be compatible with AI, obviously with players it's a little superficial but it could still give rewards for players that cooperate in multiplayer as well.