A very clever premise! You've put together something that conjures the imagination. The starting scenario helps drive the mystery of where the story will lead.
Seems that the increase of initial skill boosts are based on reaching checkpoints rather than experience via retries.
After the second playthrough it becomes apparent that the monotony seems to penalise exploration if the story is to be railroaded by means of checkpoints.
For a number crunching game; the rule of thumb is generally to reward failure. Not quite so for here. Having to retry without any secondary benefit because of a 'mistake' feels like a waste of player's time.
But overall, there's a lot of potential to this! Thank you for sharing your creative project with us.