Ok, its just a 4x game, but wouldnt it be nice to have an opportunity to not kill millions of creatures while taking a planet ?
Reasons:
1) Realizm. Accualy I dont think that whole planet needs to be perished at all. Its all about money. Do emperor cares who pays it ? And I dont think that everyone on the planet would choose to die instead of paying taxes to other race.
2) Gameplay. I think gameplay would be more great if to provide option (like in Total war) what to do with city(planet) population (slaugher/conquer).
3) Cruelty. Well.. even for game that kinda too much.