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.

Which is basically my point!

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.

yet has no metadata or any semantics, its basically just how you layout text ...

it can, using plugins. i.e. i use schema.org's things as fileClasses, which are enforced using a metadata schema for attributes which are extensible and excludable. My ontology is based on FRBRoo and I have link visualization for ease of reading.

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

it works well for laying out information for reading, and has some additional markup beyond just layout (unlike markdown), I'd argue it is fairly rudimentary and not extensible.

It's extensible in other ways.. but either way i'm moving back to Obsidian due to constantly tinkering and trying to improve my "experience" on Emacs. Obsidian gets me 90% of the way there without much fuss. It has far better image handling, and with Canvas - the possibility to lay out my own notes in various configurations is nigh endless.

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.

So what would you prefer?

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