At least with three countries the two sides that have less players can gang up on the the side with the numbers advantage.
If you guys remember the Old MA, all it took was for 2-3 large squads working together to make things happen on the map. Well, one of the reasons the old setup would get imbalanced, is that where the large majority of people flew for one chesspiece, and stayed there, A few of the squads would rotate and fly different countries every tour...from time to time, they would all happen to jump to one country at once. Then, you would have a large, old style MA that was out of whack by 50-75 players or more...and then, you had the steamroller.
I would think, that with 2 countries, The fights would be pretty large...If you had a 400 or more player cap, and the sides are roughly equal, then you are looking at + or - 200 people going into the same fight(or in a small area.) Now, with that same cap, But you split into
4 countries, you are looking at + or - 100 a country...this might open up some better oppurtunities for front lines to spread out. The fighting would be along more than 1 common front, so people would be a little more spread out. It would also hamper the 2 countries ganging on 1, because you will have a 4th state to contend with. Otherwise, the only way you can inhibit ganging, is to go with 2 countries.
