I think I'm a bit confused what exactly affects your stats and in what way? I know your character creation is not finished yet, but since apparently your stats affect the currently available routes, there must be some way to set or change them. But I'm not sure what that way is.
Your choices in the beginning and throughout the game affect them so far. I do have plans to allow players to manually adjust their stats in the future after earning unassigned ones in some way. Currently the ones that affect your stats the most in the beginning are during the intro when you are making choices with the orb. I'm working on getting some sort of guide together for the things choices affect so stay tuned.