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.