Markdown is one of those "worse is better" computer pop culture things that raise to the top, despite the existence of better tools.
I dare anyone to write a scientific paper or book using Markdown. In Asciidoc it's doable. And before you say that a markup language is the wrong tool for the job, let me remind you that nowadays authors might want to produce different formats (HTML, ePub, text-only) from the same source file which is difficult with LaTeX.
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.
I think it's more the case that there is no good general-purpose solution yet, and a bunch of people use Markdown because it's easy within a very limited scope, so now you have to deal with Markdown's near-ubiquity if you suggest something else.
I would never try to write a book in Markdown, no matter how extended; but considering the HTML produced by asciidoc|tor, you might also say "don't use AsciiDoc for simple Web publishing."
What I find much more fascinating is the question why there is no good general-purpose format that works equally well for blogging and for scientific papers and for books?
I dare anyone to write a scientific paper or book using Markdown. In Asciidoc it's doable. And before you say that a markup language is the wrong tool for the job, let me remind you that nowadays authors might want to produce different formats (HTML, ePub, text-only) from the same source file which is difficult with LaTeX.