There's a recent thread on Hacker News about an article about some slight annoyances in Markdown syntax. Lots of it is about the loss of functionality when going to HTML, and it even suggests including HTML in Markdown documents. It's true that Markdown is usually rendered to HTML, but it's not that hard to go to other formats (such as LaTeX), and it's that use case that I really like with Markdown. MediaWiki markup fails this pretty badly, and is almost always strongly tied to HTML.