Casus Belli mechanics should probably be implemented sometime, along with occupied locations, so the territory only changes hands at the end of war between human forces. Probably doesn't need to be as complex as CKII/CKIII/Stellaris' approaches, but it doesn't seem too historically accurate for an entire empire to consume another in a giant war. And having cities only switch once might help a bit with nobles maintaining their positions despite their cities being invaded.
Not sure it can make it for the next version, as we're already going to try to add so much, but it would definitely make combat a bit better. Certainly there should be a "crusade" mechanic, because current if a nation is afraid of dark nobles they'll invade their country, but then give those very same dark nobles a vote in whether or not to pronounce them guilty. It means that invading a dark nation can suddenly just add a bunch of dark nobles to your population who then doom your nation, despite people being aware of them.
I also like the idea of reputation being 'at stake' from taking actions. We tried for a bit to have every vote be proposed by a person, whose prestige would change if the vote passed/failed, but it just made stuff more complex. Having the leader's prestige be affected by war outcomes could help.
I was also thinking of an agent who would benefit from deliberately losing wars against human nations. Will keep it as a surprise, but I think it could be fun, at least. Perhaps not very balanced, but an amusing way to play, and a game should probably try to be fun, not just hard.