I realize this is a necro post, and sorry if you've already had this idea and discarded it, but I want to make sure it was considered at least. :) I'm not opposed to branching routes/options...but maybe give an indicator in the "Report card" that those are exclusive so players don't feel like they borked something somehow when they don't get both? (A line separating the always available options above, then the 2+ either / or options listed with "OR" in between them?) That way we know it is either/or and can go with our preference. (This avoids the player frustration that I'm guessing led to a LOT of negative feedback.) Added bonus, player choices in the scenes then allow you to potentially set flags for future content based on the choices made.
Love all your work I've tried so far, btw, and if finances weren't stupid tight, I'd be purchasing basically all of it. If my own ship ever comes in, you'll def get a piece of the action lol.