Following with the idea of Aknimitz about two arenas with different maps. What about the next variant?
Two servers, each one running one MA, each MA with the three countries and each MA running a different map. Each MA simulates a theatre of operations related to the same war. To win the war, all the bases in both maps are sumarized.
Once your countrie is erased from one of the maps you are not hopeless because CV groups are the only units that can be sent from one server (theatre) to another. The maps has several preconfigured "travel" zones and spawn points (one spawn in the map per every travel zone on the complementary map). That is, zones from where the CVs are sent to the other server and places where the CVs spawn in the other server. Both servers should track the CV groups as common units.
From each MA, each player is able to check the situation in the other server in a map showing only friendly and enemy bases, as well as the number of players and friendly CV groups.
A possible situation could be countries A and B present in map 1 and countries A and C present in map 2. The war progress may derive in a two side war in each map and several naval operations trying to get a beachhead in the other map.
This way we may have:
1 - Two side war in some cases.
2 - Population distributed in two servers.
3 - Two maps at same time.
4 - An interation between the players at one servers with the players at the other one.