I wonder, is it possible to break all the story segments into individual files and only upload what's necessary for the next version at the time?
For PC, this would mean less uploading the full game every time and easier for people with monthly bandwidth quotas.
For Android, the same advantages as well as being able to finish a character off then delete the associated files (or push their story to whatever point before it's locked behind another character's story and you can put a disclaimer on the individual story downloads saying something like "X requires Y and can spoil Z, so try to play them concurrently").
I'm unsure of how modular RenPy might be, but I know from Lua it wouldn't be hard to reference ifexist arguments for physical files or save file variables.