The difficulty with fighting on top of a building is that ground units exist on a height map. So the height map would need to be altered be at the top of the building. Another thing you need to get your head around is the scale. If you could imagine a 5 story ACU, standing on top of a Skyscraper, it would be like King Kong. There would be barely enough room for him to stand. You will notice that the battle in the intro movie was fought on a raised platform, at a space dock. Not on the buildings, which the platform was amongst.
You will need to accept that with the scale of the Sup Com universe, most of the fighting will be among buildings, not on top of them.
Another map you may wish to review would be Fort Clark, in the first mission. You will notice that it is constructed with a step-change in the height map. The cliffs are then rendered with tall wall sections. A similar technique could be used to get the effect you are looking for. By using a taller model, and using decals and textures to render the roof top, upon which the units can stand.
I'm also toying with the idea that building models could have defence weapons, as a way of getting the 3D land battle, you're looking for. Essentially, the Building would have a collision box, and massive HP, but not be targetable. Hence capturing the towers/buildings would allow defences to be installed on the building. This could be done by creating a fully detailed unit blueprint for the civilian building. The difference is that the building itself would construct the turrets - just like a UEF kennel constructs engineering drones.
However, the turrets built on it would be targetable, (possibly even targetable by Air to Air units
. So you'd have turrets shooting units on the ground, turrets shooting air units as the fly-by, and fighters doing strafing runs on the turrets. ... I'm starting to like this idea 
