I wish they'd balance it more on top of OP's idea, by making it very punishing to use super weapons in terms of aftermath. The fallout it would have diplomatically shouldn't be taken lightly, unless you think you are really prepared and you have allies that support you (probably genocidal species like you) like the axis power in WW2. How nuclear arsenal protocols of countries are set up is totally emergency based and it's an end-all scenario. But that's because they have more than one nuke. So if you think one super weapon isn't going to cut it for your surprise blitzkrieg (end them before they can prepare), then one should hold off on that super weapon card for now, unless they are losing the war and need to use one desperately. <- that's the kind of tense atmosphere the super weapon should have when we are using one or considering to, in a game like this. It should be very very sensitive.
I would also like it if, when several empires have such super weapons of different kinds, they could have a nuclear war. Or whatever it's called then. Maybe "Black Hole War" is more fitting there.
The empires that didn't act in the war would fear the winner (if such a thing exists in the end) because they could use their weapons on the other empires too.
And when the empires are too highly advanced in technology, but probably don't have enough planets to compensate the enemy's weapons that are equally advanced, they could die. All of them. Maybe a few planets, filled with radiation, causes some mutated wildlife or former members of the dead empires to emerge and reconquer space. That would be both interesting and... strange... to see the mutated remnants of a formerly powerful interstellar empire rebuild their worlds and then, hundreds of years later, once again construct super weapons and start the next no-winner war against the mutated people of their former enemy.
Generally, I'd love to see not-necessarily-lategame events to happen when a super weapon was used.
Any weapon that creates radiation has the chance to mutate lifeforms on a planet, maybe causing them to gain intelligence (or lose it).
The puppies could be the next intelligent species of planet Earth!
Weapons that destroy entire stars could give a distant civilization a hint about where to search for new species to enslave.
The puppies are indeed in a dangerous situation!
A black hole creating weapon could accidentally create a wormhole instead, leading to another artificial black hole in the same galaxy, so it changes the political landscape a little (That's especially dangerous when both war participants use black hole weapons!).
The puppies can use these artifacts of ancient times when they start travelling through space.
A wrecked ship could crash on the homeworld of a pre-FTL civilization, giving it the necessary technologies to conquer space and exist as another empire.
The puppies can go to space now!
The homeworld's super weapon arsenal could be sabotaged by well enough trained agents, so the homeworld (or any other arsenal world) would be destroyed and the super weapons would be too.
Nobody expects puppies to be enemy agents trying to blow up entire sectors by sabotaging super weapon arsenals...
