Yes, I understand what you're saying about the care needed in scenes, especially since you've created many choices (it reminds me of when I was writing my game with more focus). Anyway, remember that at some points you'll need to create "filtering" points (where these branches and paths somehow intersect), otherwise things will start to get so out of hand that you'll lose control of the story (if you end up with 20 branches, this will continue to multiply if you don't create this filtering point where they meet).
But anyway, I love how you're guiding the story and I hope to see more and more of your development :D