The Prince is essentially the classic Roguelike protagonist, clearing the dungeon in one life. How else would he have left a Rogue's Legacy?
While it would make sense why Johannes has the King as the only recorded enemy that he killed in his game over screen, in the terms of actual gameplay, the King is the only enemy you have kill when playing as Johannes in the tutorial (you can skip the knight if you want). However, if the 16th Journal entry is to be considered, Johannes may have forgotten most of his quest, including the enemies he has slain along the way.
The 16th Journal entry marks the slow descent of the Prince into insanity as he has troubles remembering his past and his family. But the last line implies a What If? he killed one of his brothers inside the castle?
What if years have passed since I first entered these walls? It is true that I am becoming more proficient in clearing monsters, but it feels like an age has passed. I have even forgotten what my own kin look like. What if they think I have failed? What if one of my brothers has beaten me to the cure? ...And what if I mistook them for a monster.
By separating romance from marriage; they can marry the opposite gender to produce an heir, but the person you meet together with your children at the end of the game could be a seperate character who is the same gender you're romantically involved with.
They don't. Every kid chosen comes from a pool of three, so if you play as a gay character, 'their' heirs are actually the children of their siblings.
It makes sense for Charon to always be in front of the castle, since he's a psychopomp and all that, but what about the Smith, the Enchantress and the Architect? Are they immortal? Are they descendents of a long line of identical people? Are they personifications of their jobs?
