Nukes are boring, expensive, and easily counterable. So how about adding more nukes? Maybe not nukes, but interplanetary missiles, with different warheads? Something like a seismic nuke, that will drill underground and that explode. Explosion will be not as powerful as regular nuke, because missile has some drilling equipment, so there are less explosives. It will do far less damage, but over a wider area. So you can make your enemy busy with repairing his base. Or a nuke that can destroy asteroids? Or just a smaller tactical nuke, maybe even without ability to travel between planets? Or a nuke WITH NANOBOTS?