I would say that markdown for informal writing is fine and I like Markdown for many thing BUT if I need formatting LaTeX is a better tool. I have always waited for a new system but its hard to replace what works (With some cursing and banging on the desktop). Writing Math equations there is almost always a need for formatting within the document.

To me a math equation is just another plot. I love making quick plots but when it is my name on the document I want to be able to control every line and space.

I really like Scribble a Racket made document language is certainly the way to go but it will take a while to get broader usage. https://docs.racket-lang.org/scribble/

EDIT----

Math Library - http://docs.racket-lang.org/scribble-math/

What Scribble does really well is you write your document and it is a one line change to change the output. It can output to MathJax or LaTeX or Markdown or PDF etc....