For a rough draft this is already looking pretty great. Obviously you'll be cleaning up the arrows and outlines a bit, and like you said, giving an overall header and so-on, but I'm liking the look in general. I'm not sure I buy the floortile background entirely, though it is a clever idea. A solid color, even just black would probably work better, but experiment on your end and see what looks good. You may win me over.
I'd also say: let's stick to JUST the scenes, ie the stuff with art. That's what people are most looking for, and I like to keep the other stuff a bit more obscure. Also, though just a draft obviously, this chart is actually inaccurate: Lying to Mahir is, as the Silicon Valley people love to say, "orthogonal" to any of the actual scenes with art. It DOES unlock some text stuff in the plaza, but for simplicity and fun of discovery, again, let's leave that stuff off.
I'm also mixed on having everything connected in one flow, though I suppose that makes more sense for a visual rep. Maybe one straight line, horizontally or vertically, representing a totally un-eventful playthrough to a win at the end, and then branches off that for each event, some which re-join the main line, some which don't, and some of which branch off further as appropriate. But a bunch of stuff kind of clustered around a center (or side-aligned) line. That's the added challenge of doing a graphic though, you have to ponder how to actually express the flow accurately visually instead of just briefly mentioning the conditions for each scene.
And yeah, you can give the pixel look a try, but it isn't required, just a possibility that might be neat depending on how it ends up looking.
Can't offer much on font, typography's a weakness of mine, as shown by the...mediocre credits. Font seems fine though.
And thanks for all the work put in so far, do think this has potential.