At this point, I'll be keeping most of prologue and will just be removing some of the redundant/repeated dialogue, so the prologue won't be too different. But I'll also be adding a quick third option of summarizing it - (Probably with the Goddess summarizing it for the player in a rude/condescending manner).
Though, this will probably be added in v0.05 or 0.06, depending.
And as for adding an origin to the Player to make him more proficient at certain task or skills, I probably won't. Simply because it'll kind of interfere with the story/the reasons why he was chosen in the first place by the Goddess - (Aka the player being seen as completely useless in her eyes).
However, I will be adding/working on light rpg mechanics, where the player can improve himself throughout the story. Like him training with Cecilia at the Barracks etc.