Great suggestions. I'd like to add one little one (maybe it's already there and I'd forgotten- haven't played in a while).
I'd like to see a race option that would determine how well occupied planets of different races (e.g. you invaded their world or their empire surrendered to you) react to you as their new rulers. For instance, I've played games where I conquered a few different races, and no matter what, they continued hating me for the rest of the game. Their homeworld was always on the edge of rebellion, even with Urban Pacification Centers and troops, and any time I shipped them off to colonize new worlds, the new colonies would rebel in a few short turns.
Is there any way to combat this, other than lots of troops and facilities? I'd like to see a race stat for "Kindness", "People Management", or something along those lines to ease racial tensions (or make them worse if you want to be the cruel overlord type- and hey, who doesn't?). Or maybe have tensions be lowered depending on how close the society types are. After all, it's easier to take being occupied by people with similar cultures/philosophies than by your antithesis.
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Concerning martial
valor, merit lies more in
dying for one's master
than in striking down
the enemy
-Hagakure