That is kind of interesting....
I'm assuming that Sins has some type of triggering / scripting language since it can spawn pirate raids, Returning Armada, and the TEC Insurgency power.... and there is something the logic that controls AI's is to work with.
You could create a large number of unique structures that are capturable structures that have a diverse selection of RA like powers that trigger spawns targetted against your opponent much in the way a pirate raid is triggered. The game would then be about trying to defend your holdings while capturing these triggers to create attacks against your opponent. Or attacks could launch at regular intervals and depending on who has captured and is holding these locations would determine their victim.
Instead of Heroes, each team would have capital ships with diverse powers and the ability to capture things. I'm also guessing that players would have some limited ability to build stuff and unlock new structures via tech.
If you want your capital ship to be able to "resurrect" it should be pretty easy. Your capital shipyard has the ability to make capital ships for free, but you have no way to upgrade your capital supply capacity past 1. Then you give the capital shipyard the Progen ability to restore level. If your Hero capital dies, just rebuild it and use the restore ability at the shipyard on it.