The main point of Markdown is that it has a very important feature that other languages don't have: it's supported in a lot of places. Most of the alternatives mentioned in this thread or in the article are things that require custom tools, that can't be used in most of the places that currently do support markdown. It's common in a lot of places. Even Google Docs has a well hidden feature that allows you to paste markdown.

It's one of those good enough things where the things it doesn't do are outweighed by the notion that you can just use it pretty much everywhere.

It's a Betamax vs VHS type discussion (both are at this point obsolete and forgotten). HTML used to be pretty limited as well compared to things like SGML or any of the wonderful things people used for structured documentation in the eighties. Most of which are long forgotten. It still is pretty limited compared to those probably. But the point with HTML is that that's what browsers supported and not other formats. Many of the limitations were addressed over time.

Markdown could be improved in a similar way over time. We have ambiguous standardization, lack of features, mutually incompatible implementations, etc. The whole thing actually resembles HTML4 before people started addressing such concerns. Evolving Markdown seems like the easier path than replacing it with something else.