Personally I think Markdown sucks, although perhaps less than Haddock markup.
Still:
* No document meta data
* No code block meta data like language for syntax highlighting
* No tables
* No footnotes
* HTML fallback is insecure
* Confusing syntax (is it []() or ()[] for links?)
* Syntax that gets in the way (maybe I don't want *stars* emphasized)
* Above point leads to non-standard dialects like "GitHub Markdown" (no, GitHub doesn't use markdown)
* Not extensible, leading to even more non-standard hacks and work-arounds (GitHub Markdown, Pandoc Markdown, other Markdown libraries have their own incompatible extensions)
* Not well suited for web input (e.g. four-space indentation for code blocks), although not that important for Haddock
An important thing to note here is that no, Markdown has *not* won because no one is actually using *Markdown*. They're using their own, custom and incompatible dialects.