I suppose it's harder to cross-reference and find things, though I suspect you could utilize some sort of organizational system to mostly overcome that.

I really do think pen and paper will slowly regain prominence; I personally find that it can be much more liberating than digital media.

It's great to be able to use the page as a canvas, writing wherever you want, without having to meet the constraints of a text editor or the likes. Doodles help to visualize and understand problems, too.

Tangent for macOS is my current go-to for note-taking, and it works quite well: it's mostly just a Markdown editor, a tree structure of folders (which is really just a normal folder), and the ability to cross-reference and embed images.

I suppose the primary problem of note-taking apps is that they sort of have to be opinionated in some way to be useful (that's been my experience, anyway.) Markdown files are also guilty of this: they constrain you to a certain layout, which can either be a negative or a positive. Anything too complicated can be off-putting, whilst anything too simplistic can also be limiting.

It's a surprisingly complex field, and it could explain why there's so many different apps for it.

What is complicated about organizing written notes?

No search, no making space in an existing page, no moving text around, cumbersome to take it with you everywhere, unlike a phone.

You don't really need most of this, or it can be solved simply by thinking and remembering.

By that logic you don't really need paper notes either.

Not complicated, but many people have never learned how to do it or developed a system.