This is an old topic, but still very relevant and not resolved yet I think. Mathematical formulas are very important in several contexts, and having a standard syntax in CommonMark would be very desirable.
LaTeX is probably the most used syntax in the diferent Markdown flavors, however in my opinion LaTeX is not very readable (even a simple formulas like 1 / 2 = 0.5 is written as \frac{1}{2} = 0.5) which is against the main design goal of Markdown. For that reason I think AsciiMath would be much more readable:
With AsciiMath the natural formula is used instead 1 / 2 = 0.5 (which is pretty printed by MathJax), and it also provides greek letters like \alpha. AsciiMath supports pretty advanced mathematical symbols (and those continue to be highly readable) so I think would be enough in the vast majority of the cases. My team uses AsciiMath inside Doxygen comments (using Markdown) as internal documentation of our code (i.e. not usually read as HTML by directly as plain text in the source code), and the readability is now much better than when we used the LaTeX syntax (which is the usual approach in Doxygen).