Void Dwellers could be so much more fun

Think Quarians from Mass Effect. They don't have planets or stations or even space. Just ships. Colony ships take the role of population centers.

Their mining slowly and permanently depletes the resources in systems as it goes. Nobody can close their borders to them, but of course have the opportunity to dickpunch them if they're unhappy with having their resources depleted. Said mining is done by colony ships.

Colony ships are larger than battleships and take naval cap, but are smaller than juggernauts. Have a shipyard in each. Cost is of course balanced to be fair with what they offer. They're pretty slow, such that even a juggernaut could pretty easily run them down.

You can spread your fleet as much as you want, of course that means you lack the ability to defend it properly. To keep you from making a murderball that nobody can attack, empire sprawl is impacted by how much your total empire is consolidated. The tigher you pack it, the more it'll hurt you.

Then Paradox can permanently fix habitats by simply deleting them from the game.