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i bet an equal cost batch of LCs with psy-subverters or computer-viri would have really ruined the BMs day. I would contend that the BM needs a custom built stellar manipulation device that is basically a big anti-planet weapon that is not destroyed after use. either that or a giant ray that simultaniously ruins planet conditions and depletes resource values by something like -150%
Try a Core-Mount anti-planet weapon like a neutron bomb. You could reduce the value and conditions to zero instantly, as long as you can get to the planet with one movement

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In P&N, there is a defense against weapon & shield destroying damage, and I will either have hardened MC components available, or make the allegiance subverter be a hand-held boarding party weapon. The third option is to embed the MC into the planetoid core, so you can't subvert them, only their "escorts".
I really hate easy takeovers... I think that if you want to capture a ship (for tech, war duty, money, whatever) you need to work for it. Strip the shields and try to pick off the MC and SDD. You have to outnuber your enemy and get some lucky hits on the critical anti-capture components.