Bizarre idea, but what about a side commentary to the game? With the jewels marking the progress of the game, you could easily create something along side that said, "Play when after the 2nd green gem" as a for-instance. Only place that gets tricky is the split between Winkie country and Quadling Country, but I suppose that could be a preface for those two branching options... (Unless they did like me and try to play both at the same time, which results in one cut scene upon arrival at the second and... I think I'm starting to spoil the game at this point.) Just a proposal of a way you might do it, if you truly wanted to.