Bit weird to say you're going to talk about syntax and then complain about syntax highlighting in markdown, which is a rendering problem.
Markdown is perfectly well suited for whatever documentation needs you have imo/e. If you need complexities not standard to CommonMark you tweak your renderer or inject some html as a preprocessing step, for example adding mathjax for formulae or say, a syntax highlighter.
Markdown is simple enough to use and simple enough to extend for your deployment. Haven't had any issues with very complex docs started in MD.
