Huh, interesting. I do know someone who is quite happy to use Scrivener, so if it works it works I guess, but it seems to do way less than I thought it would.

At this point something like org-mode or markdown sounds more useful. At the very least you could annotate scenes with metadata and read this metadata using other programs. Should be reasonably doable to tag scenes with the characters in it etc. From what I know of org-mode it could do quite some magic with just that info.

I reckon LaTeX is also a good choice, though it's tricky for other tools to read, you'd basically always need to compile it first, or stick to simple LaTeX.