I've been wondering if there was a way to put atrocities into the politics of the game. No, I don't mean the poster on this board, either.
Something like bombing a planet flat should have negative impact on both the target race (for obvious reasons) and other races (who might wonder what you'll do to them) based on their personality profile. Psychotic and xenophobic races might not care about what happens to another race, but Honorable races probably wouldn't react well to a race that commits genocide.
Maybe there should also be a few Propaganda projects in the Intelligence section to offset it. You know, manufacture a bunch of bs about how your admiral exceeded his orders, will be punished, a nice guy like you wouldn't do that and they did it to themselves, etc.
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"What do -you- want?" "I'd like to live -just- long enough
to be there when they cut off your head and stick it on a
pike as a warning to the next ten generations that some favors
come with too high a price. I would look up into your lifeless
eyes and wave like this..." *waggle* "...can you and your
associates arrange that for me, Mr. Morden?"