I think it’s fair to say that virtually everyone with knowledge of and an opinion on the matter would agree that on the technical merits Org mode is clearly superior to Markdown. The differences in syntax are trivial and don’t really matter. What makes Org superior is Babel—enabling the inclusion of executable code snippets that can effect the host document—and a single, official definition of the language as defined by its reference implementation. It’s also arguably true that Org has a better export system but Pandoc neatly fills that gap for Markdown.
Some people point to Org’s tight integration with Emacs but lots of editors, including Emacs, have “modes” that similarly integrate Markdown. Others claim that Org does a better job with metadata.
Markdown’s claim to superiority is that “everyone uses it”, making it a sort of lingua franca of markup languages. While Org mode is, as a practical matter, restricted to Emacs, Markdown can be used with any editor so of course its use is more widespread.
But what if you’re an Emacs user? I can’t think of a single reason to prefer Markdown to Org mode1. What to make of this then? Hezha98, an Emacs user, wonders if he should switch from Org mode to Markdown on the grounds that Markdown is more popular. That’s a silly reason, of course, but what’s surprising to me is that many of the commenters support his changing to Markdown. Not one of them used collaboration—which, I suppose, might be a reason to use Markdown in Emacs—to justify their choice. I don’t understand their choices.
But, of course, whatever you prefer Emacs is there for you. The Org mode support is better for sure but Emacs also supports Markdown mode. As always, Emacs has your back.
Footnotes:
There are some people who simply prefer the Markdown syntax but they’re pretty much outliers because, as I said, the syntax differs only in trivial ways.