RestructuredText has generally worked nicer for me that Markdown. Especially when combined with Sphinx you can easily embed LaTeX math structures as well.

Having that said, depending on the scale of the paper I usually tend to go back and forth between RestructuredText and LaTeX. When it's large and might need some fine tuning it's better to use LaTeX, when you simply need to jot something down... no need for the complex LaTeX setup.