I've only played the game for about 30 hours now (total) and I haven't run across these options yet, but if they are actually in the game I'd love it if someone would tell me. Anyway.
My first suggestion is not gameplay related really, but would help tons for immersion: the ability to bring up the stats on the races that make up the population of a planet. Immigration and such would have a bit to do here, but mainly its for planets that you take over through conquest or rebellion. You KNOW those planets have X billion of people that are of a different race, but the game doesn't even notice. It would help to make the races more distinctive if you had something like "Colony population: 90% Yor, 10% Terran". On the gameplay side of things, come to think of it, planets that are conquered should have some sort of scaled morale decrease according to the percentage of the population that is of the conquered race. It doesn't really make sense that after my fleet turns a planet populated by 10 billion into a smoldering ruin of 3.5 billion the colony then acts just like any of my other colonies.
Plus, I'd like to blow up Class 0 planets. Make it super expensive or something, but I still want to blow them up.