The lack of a consistent standard for Markdown is a big obstacle for this. Markdown comes in various "flavors" so you end up with a quirks mode nightmare as bad as IE6-era HTML, if not worse, and you sacrifice expressiveness as part of the bargain.
Potentially unpopular opinion, but GitHub flavored marked down is almost inarguably the de facto standard, and the vast majority of markdown in existence is GitHub flavored. We should just embrace this.
