I disagree; I think a system like Wikipedia shows that a textual and visual format like markdown provides the flexibility to convey pretty much any information. For any formal and semantic storage system, you will probably spend more time adapting it to each specific use case than to actually fill it with content.

Formatting and knowledge management are somewhat orthogonal concepts, aren't they? You store information in a textfile, have rendering thereof based on Markdown, and another layer to reference and index files.

The thing is that if you want something portable where if the app goes down you can still use it, you don't have many options. There aren't really any formats that support the kind of note linking used in PKM by default, besides maybe HTML but if you think that's a better solution than markdown I think we have a difference in values that can't really be remedied here. So assuming you're not using HTML, now you're looking for a common format that is easily parsed so that you can have links, and also simple enough that you can look at it on pretty much any PC. That really only leaves markdown and plaintext (and maybe JSON? But again, same as HTML, that technically works but it doesn't really fit the bill here), and markdown is just better for notetaking

I agree. Markdown is way too much overrated as a multi purpose document format. I find it very limiting even w/ Obsidian. It would probably work well for some text-people, but anything more complicated than 1D character stream won't fit well into Markdown.

Org-mode works well. It is essentially just a markup like Markdown.