Don't know about stacking. The maps have a lattice system. It shouldn't be too much trouble for varying sizes of warships to have an area of space that other warships can't access, and they can't just park their humongous asses right over a base deep behind enemy territory, so they could be forced to only go as far as the front line, making them always a part of the main fight. But they should be destructible, making them risky to bring to a fight. An outfit wouldn't want to bring their ship into low orbit unless the skies are safe from ground emplacements designed to punch holes into warships.
The benefits to bringing in warships, of course, would be orbital strikes and a mobile base that offers vehicle deployments as well as troop deployments.
Though I see them primarily being deployed in a Planetside 2: Starside Intercept expansion where we're fighting over asteroids, derelict Vanu colonies, and orbital stations. There'd be room for the ships to work with up there.
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