I'm curious what makes you consider it non-ergonomic? For the things both support, I don't remember that many differences. Org shines, though, for all of the other things it also supports. In a real sense, it is more in the same realm as jupyter than it is markdown.
I think org-mode has several fairly orthogonal use cases, including literate programming (your Jupyter reference), outlining, markup, task management, spreadsheets, and many more. And the community has done an amazing job of implementing all of these really well, each for itself, while still maintaining a working ecosystem. But I only use a small subset of that when I use org mode. The amount of metadata that needs to be included in a full-blown org-mode document seems to be increasing, and I feel more and more like I am writing a specification with verbose syntax (and personally, I find "#+BEGIN ... #+END" blocks or similar keywords unappealing).
Literate programming is rather distinct from notebook style, though? I can see surface comparisons, but they are very different.
I can see not finding the markup appealing, but that is why you would export for viewing? And, outside of moving some of that to a binary format, I don't know how you could get this level of stuff in band? I suppose you could strictly hide it in view? Would probably still want the markup in data.
None of which is answering what makes it non ergonomic? Basic text with an actual table format is about what I'd hope for it to be. What is off?
Links are different. Everyone seems to redo that idea. Rst files, I still always get wrong on first tries.
I think that's really the key thing, and I didn't realize it until only recently: org-mode fits a Jupyter mental model better than a Markdown (or outliner, etc.) mental model.
It's great for what it is, but what it is doesn't 1-to-1 map to much else.
I think this makes sense. If you are viewing it as marking up a static document, then a ton of the affordances in org-mode make little sense. Most of it is about interacting with a lot of data that happens to be represented in plain text.
For a lot of us, that focus on the plain text is important. As it helps keep us focused on all of the other affordances that we have grown accustomed to in emacs. As soon as you move things into a binary format, you are likely giving up on a lot of the other tools you have. There can be reasons to do this, of course, but for most data that you interact with at a personal level, most of those reasons have been overcome by the power of the personal computer.
