The problem with Markdown is its embarrassingly poor support for highly structured documents. Something as simple as writing a multi-level list interspersed with complete paragraphs is a nightmare to do in Markdown. Tables and images aren't a big improvement over LaTeX and require special syntax to scale and position.

I'd rather use Word for simple documents so I can enjoy drag and drop and graphical image positioning and scaling and easy tables and leave LaTeX for complex documents. Markdown is the worst of both worlds.

However, I could see myself using the much superior Asciidoc (vs Markdown) instead of LaTeX, but unfortunately, the worse-is-better philosophy is still alive and has made Markdown the defacto simple markup language, and tool support for Asciidoc is as poor as LaTeX, so I just go directly to LaTeX instead.

AsciiDoc is essentially XML DocBook with a simpler syntax. It has enough structural constructs for large documents. Also DocBook was designed as master format, and is easily render-able into various outputs forms like for printing and for web pages.

I’ve found writing in markdown and converting to other formats to be a very frustrating experience. It only works well for exceptionally simple documents. But as soon as you want something even slightly complicated it falls apart. Side-by-side figures, multi paragraph lists, footnotes, and numbered bibliographies are all trivial in latex and are a huge pain, if not close to impossible with markdown. I’ve wasted huge amounts of time on this.

On the flip, the latex syntax for super simple documents isn’t really onerous (especially if your editor fortifies the different elements). So I just end up using latex for everything.