Great idea, great design! As I think markdown is good only for write simple texts (AND NOT FOR ADVANCED BLOGGING), a novel writing software would to be a choice; because authors don't use richer text format than markdown, as Nick mentioned.
Markdown is pretty good for advanced blogging if you use it as a superset of HTML, as originally intended.[1] That way you get simple syntax for the stuff you're likely to use most often and can still implement more complex formatting when you need to.
I have the complete opposite view as you. Markdown is for advanced blogging and since novel writers don't need advanced html formatting they don't need markdown.
Ebook formats are mostly HTML and (a strictly limited subset of) CSS. So, given that a book will eventually be rendered down to HTML, markdown isn't really that bad of a choice.
Especially since things like tables can actually be useful, depending on what you're writing.
