Make true roaming open world pvp.
If you look at warhammer, they have a good idea, the problem was it was poorly executed. You shouldn't promote zerg play, you should promote organized group play.
If you add objectives and bases that can be captured which take control of zones to give bonuses or access to specific content you need to make the zerg spread out.
If you have 2 bases in a area, and 5 smaller objectives in the zone as well. In order to capture the base you should have to own 3 of the 5 objectives. You must maintain control of these 3 objectives at all times to make the base remain vulnerable. This would cause operation groups to have to spread out and break down there group in order to hold separate objectives while raiding the base.
In cases of population imbalances on servers. You can add a AI assist mechcanism where the Empire or Republic drops off vehicles to the side with the lower population after an alloted time has past. The pop imbalance fix has to be looked at closely and should only take affect in a 1.7+ : 1 ratio, too small and one side gets too beefy, too large and you still can't overcome the odds.