ReStructuredText (.rst, what Sphinx uses) handles it quite well. I understand why Markdown became so popular (super easy/intuitive) but what I don't understand is why so many documentation systems use it. It's quite limited... On purpose!

You want to support simple text features in a forum or comments on a website? Markdown is perfect. You want to support basically every documentation feature imaginable while still retaining reasonable ease-of-use? ReStructuredText is the way to go.