Factions and Politics
Governments in Stellaris may hold a grudge against you for centuries for your atrocities but pops and factions are very quick to forgive and forget. There are no revanchist or irredentist factions that make trouble when borders change, nor variety within the factions themselves. I’d also like to see factions have their own tenets and goals and different ways that you can deal with them. There have been a lot of calls for an “internal politics” expansion, but I think that it would really be politics and culture in general, affecting both your empires and those around you.
If we were to do something along those lines, I’d also want to add some variant of factions to Gestalt empires - maybe Instincts for Hives that grow more dominant based on your behavior or Directives that compete for priority in Machine Intelligences. They’d have to feel different from individualistic factions, however. Among individualistic factions, I could see the tenets of an Egalitarian faction from a Shared Burdens empire being very different from the Egalitarian faction in a non-Worker Coop MegaCorp, and these tenets might also be used to define the beliefs of your Spiritualist factions. I’d certainly want to explore spreading my factions into other empires.
Espionage
Espionage is a related system that isn’t satisfying its promise currently, as Mr. Cosmogone reminds me during every design meeting.
It’s difficult to keep track of spy networks, is generally of low impact, and has no real counterplay. But he’s got schemes.
Pirates and Crime
Space Piracy is a popular fantasy - we touched on it a bit with the Treasure Hunters origin in Grand Archive, but they could mesh well with the Nomads idea mentioned earlier or even a factional political expansion. Crime and Deviancy aren’t terribly engaging systems at the moment either, and might benefit from wider examination.