I have never understood why Markdown has gotten so much attention over the last decade while ReStructured Text - which is a similar format but actually standardized and more developed than Markdown - gets so little.
Tools like DocUtils and Sphinx allow one to do quite a lot with ReStructured Text, and I believe Pandoc can convert it to Markdown without any issues.
If you aren't familiar with it, a good hard look at ReStructured Text may be worth your time.