We don't have to do strict Markdown, but even Markdown is transparently extensible in HTML. It is entirely feasible to write publishing quality documents in HTML/CSS3, and thus, Markdown.

I would love to see something like Markdown, but well-suited for typesetting, but with a transparent backend scripting language for more in-depth tasks. Scribble looks like a good start: http://docs.racket-lang.org/scribble/index.html

Currently, I use org-mode and LaTeX-export for this. It works well enough, but a native integrated environment would open this to a much wider audience.