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.
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.
