Zero Escape's two first games' structures are a improvement over your usual charage but it is still not a good example of how routes should be made. In those two games, it branches based on what door you open. Even in VLR, ally/betray AB game is determining which doors will be opened later. This is not plot related and imo a pretty bad way of using a branching system. It's random and all you see is the awkward shadow of the puppeteer everywhere.
I tend to forgive charage when each routes is giving away a piece of a global mystery, not just random stand-alone drama I don't give a shit about.