Markdown does not support cross-referencing of figures, tables, and sections, and doesn't have numbered "environments" like LaTeX (e.g. theorem, definition, example). It would need to be extended.

There's a slow-moving Scholarly Markdown project, but I don't know what its status is. http://scholarlymarkdown.com/

I agree with the sentiment, though. If there were some markup language that supported what academics do with LaTeX and Word, and converted cleanly to JATS XML and to nice-looking PDFs, it would be enormously useful.