Hello, I am just recently getting involved with the RPG Maker community though I have decided to pursue using the program for a project I've been working. Interestingly enough, the project started off being intended for something such as a screen play or a visual novel, and I've come to find that it is evolving into an interactive multi-platform development.
Of course, it can seem to be an enormous undertaking though I commend You, EliteKilljoy, for seeking to take upon such a task.
I've found that the challenge is implementing the 'story' into various mediums (literary & graphic). So, when it comes to adapting it to a visualization, I remember to consider the moments of the piece which are visually captivating (like a movie), and possibly emphasize major instances which have a catalyzing affect upon the the story and how it transitions. Characters (of course), and how they appear (Their mannerisms, gestures, development, etc.) are always important. Unique environments, objects, and more which are specific to the story. Scene intro's & outro's as well as scene transitions, deciding between using linear, non-linear, or other methods of story-telling. What kind of perspectives are used? (are we following the main character? Are we following the roles of every major characters, "good" and "bad"? Or do we have sort of universal perspective where we, the reader/viewer, are just merely observing the story)
There's a lot that goes into a project like this and I personally have found that utilizing the ability for the reader/viewer to interact and actually take part in the story as it unfolds is a great way for us to move from observer to participant when it comes to storytelling. It reminds me of those old 'choose-your-own-adventure' books!