In regards to the villain and killing character arcs, I find that would be an easy solution? (unless im misunderstanding your meaning).
Ex: when you take over the brain, the game just ends. Same when you convince the Emperor to control the brain. No reunion camp, no city or citizens rebuilding, or narration.
I dunno if this would be that popular as you'd essentially need to build a new character to play the dlc.
If you chose a bad end, there woudnt be an epilogue just as the game currently. If the Emperor was killed or betrayed, he woudnt be an option for you to go and visit him, the same as the characters who were killed.
Certain dialogue, scenes, and areas would not be available depending on the actions made and party members you chose and what you did just like the game currently.
This is okay if the character only appears once but you can't then build an entire story around them if you could also optionally kill them before. Unless you retcon it.
For some comparison. In The Witcher 1 the protagonist gets to romance one of two characters. Triss or Shany. However once you play the sequel: The Witcher 2 the game ignores your choice in the previous game, Geralt always romanced Triss no exceptions. That's likely what they'd have to do with a DLC they'd just need to either ignore your choice from the previous game, or make the character be very minor to the point where you could cut them out without much difficulty.
