I'm not sure if this counts but too many characters are dying from being imprisoned. This seems to because cause of the improved genetics thing that made more characters to have health less than 5. Either the baseline health needs to increase or house arrest needs to become the default method of imprisonment. This whole thing is exacerbated by the peculiar way ai fight wars. Nobody seems to fight pitch battles and instead only want to besiege the other's territories.
Funnily enough, my experience in my current game is exactly the opposite. As a Byz emperor I have noticed that most of my prisoners live on for years on end in the dungeon, which stretches on to decades if they are put in the oubilette. Yes, the oubliette for me is some sort of deep freezer which keeps people alive. It's recurrent, but the best one was when I had a bunch of rebel counts stashed in the oubliette for decades: one died after 28 years in there, two more lasted beyond 20, every single one made it past the decade mark. All of them were malnourished and insane, but kept on living.