If you consider Markdown on its own, I agree that it's rather difficult, but you should really try Pandoc, any output is possible, including scientific papers (pandoc-citeproc is fantastic) and books. Without Pandoc, Markdown would be very limited for my use cases.
I had forgotten about PanDoc! That's true, for some time I was pondering going Asciidoc vs Markdown+Pandoc. I liked the "purity" of Asciidoc (most things you will ever want to do are built-in), and Pandoc felt like it was a non-portable collection of hacks to get Markdown to do useful things.
I wish I had time to evaluate them in more detail, but so far I've stayed with LaTeX, which I feel is not the right tool for the job for material that's not going to be printed on paper.
