Alexis Kennedy, CEO & Creative Designer at Failbetter Games, gave a talk at Pocket Gamer Connects San Francisco 2015 about how to write non-linear stories.
He started by saying that "any time you offer a choice in a game, there are about a million other choices you could be offering", and that what you need to be thinking about is which options you're choosing to leave out.
Don't go crazy
Kennedy suggested that the "sweet-spot" for the number of choices was five, which gives players plenty of freedom without having too much extra work for writers, but also said that "if you're ever not sure, give them three choices."
He also said that if you can offer an experience in your game that allows players to ignore the main quest and "rebel" against the designers, users "will love you for it", as it lets them feel powerful and more in control of the game.
You can see all our videos from Pocket Gamer Connects San Francisco 2015 in this YouTube Playlist.