Can't speak for anyone else, but for my part there is animosity towards any format, period. Documentation should be plain ASCII - or, when strictly necessary[0], UTF-8 - text, and readable as such with only human-generated ad hod syntax such as *emphasis* or
+------------------+
| ascii-art tables |
+---+--------------+
| + | corner |
| | | side of cell |
| - | bottom/top |
+---+--------------+
Admittedly, I'm not necessarily a repesentative example of anything.
What I see as disadvantages are: It is not possible to render it properly or have support for it beyond showing plain text. Many users might write things different from each other, which might affect how easily a reader picks up what each document's style or conventions are.
Sure you can, and indeed that's what markdown was originally supposed to do (at least as it was first described to me). The catch is that you have to treat the plain text as the authoritative version: you do not edit the plain text in order to produce changes in the rendered document; you edit the plain text for it's own sake, without considering the effect on the rendered version, and the rendered version is derived from that.
Missed this and too late to edit.
0: Which historically meant "not stupid-quotes", with a addendum for stupid-dashes, stupid-ellipses, etc, but now also includes "not emoji".
The most annoying thing about Markdown is that most of the time (90%, I'd say) it's added some kind of formatting, I was not trying to format anything at all.
I have used Markdown, Pandoc Markdown, probably Github Markdown, probably other dialects of Markdown and I kept missing features for writing documents.
I have written a thesis in rST and it worked very well, even though Pandoc at the time did not understand citations and arbitrary document internal references (both of which standard markdown does not have) in rST well enough. I had to write my own pre-parser for it. I could not have written that thesis in some markdown dialect incapable of expressing things, that one simply needs in academic writing. There was Pandoc Markdown, but it felt bolted-on and rather ad-hoc in comparison to rST, which brought all the things out of the box.
I remember also looking at AsciiDoc at some point. Not sure, why I did not choose it.
Then I discovered Org-mode. It has been a journey to uncover more and more of org-mode capabilities. Org-mode does not suffer from the same eco-system split up as markdown does. It does not have this bolted on feeling, that many markdown dialects leave me with. It usually has everything I need. In fact, I have written technical documents in it as well and have discovered things like literate programming. The tooling in Emacs is so good, it is really nice to work with org files. Good, that I can still export to primitive markdown, for anyone not knowledgeable in org-mode. Even though org files are merely human-readable plain text documents. It is unfortunate, that VCS hosts are unable to render them properly.
I would really dislike going back to markdown only. It feels so limiting to me now, that I have developed an aversion against writing documentation in an unsuitable format like markdown (talking standard markdown, probably commonmark). If there is already markdown only documentation, then well OK, I guess I can write it, although it surely will not feel great.