One way to create a choice-narrative that is more interesting and complex than a linear flowchart is to figure out how plot mechanics might be expressed in board-game logistics.
This is a Smosh let’s play of a tabletop board game called What Next. It illustrates how a card-based story can be made interactive with choices, mini games, counters, and a day/night cycle.
(Potentially NSFW; cursing is bleeped for YouTube)