Hi Nootellix,
Please dont apologize, I love hearing your thoughts! Here is some spoiler as as I talk about my general approach to decision making and consequence in my games.
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So as you know I am a solo dev and I work to keep my writing within reasonable scope. Yet I still believe in making narrative games require player input regularly with decisions that feel like they make a narrative difference. I do this largely by a combination of short term variation and long term value assessment. I may also allow myself 1 major point of structured story branching. (In ADW it was siding with the oldones or the gods, in this game its picking an LI route. this is a story multiplier from the moment its implemented so i only allow myself to do this once before the endings) So building stats like PP, EP, LP overtime will shape some short term variations (immediate responses and "variations" of the main story but do not change the main path to the ending.) They are the "seasoning" of the story that I feel like can be adjusted to the players individual taste but does not meaningfully change the dish. A cake is still a cake, whether its vanilla or chocolate. With enough seasoning, the player can feel like this cake was made to order (at least this is the goal! To have it feel like it's personalized somewhat to your tastes) At the endings is where I really have to pay the piper as the dev. for every path and every flavor I will make a separate outcome so in the case of this game, it will be based on factors such as 1.character route 2. PP, EP, LP and 3. relationship markers (trust, attraction, dependance.)
certain flags may add a longer stretched out"variation" from these main paths such as whether or not you tell Simon the mc is subject 001. He has foreshadowed meeting with Isaac, so there's a strong hint that he will find out either way. So in short, no, there's no major story path divergence. Just minor flavor variation.