Honestly I am ok with this, i find there are setups similar to this, but they never progress far because they try to give choice from the start. So for example for the amount of work you have done, if you gave us choices, others would only be on chapter 2, and potentially not even done with chapter 2.
I am honestly glad to see a fleshed out story before we are given the options to interact with the story as it seems like a breath of fresh air.
I think working backwards on choices once you complete the "Main story" is easier to think about. and gets a complete story out anyone can enjoy and not be waiting for as long. if you work on the branches early you increase your workload by that many choices. For example, not sure if you plan this, what if instead of the 2 girls competing to be the biggest they pool their catalysts into one or the other. Big differences that require 3 different stories, 1 how you have it, 2 if Sam gets it all, 3 if Alex gets them all.