I don't understand what you mean about lacking math support. I am writing math exercises using asciidoctor right now, as it integrates with Mathjax.
I would highly recommend asciidoc over markdown for scholarly work in succint plain text. Markdown is limited in its capabilities by design, as evidenced by all the different flavors of Markdown extension. It's what I would use to write an e-mail or blog post. Asciidoc, in the design of the language, anticipated extension and post-processing and has better support for using it as part of a complete document processing toolchain. After all, it's just syntax sugar for DocBook XML.
I would highly recommend asciidoc over markdown for scholarly work in succint plain text. Markdown is limited in its capabilities by design, as evidenced by all the different flavors of Markdown extension. It's what I would use to write an e-mail or blog post. Asciidoc, in the design of the language, anticipated extension and post-processing and has better support for using it as part of a complete document processing toolchain. After all, it's just syntax sugar for DocBook XML.