Aside from the software development aspect, the OP echoes a lot of my thinking at times.
> In practice 95% of the use cases ... unbundled into disjoint apps, and the lack of centralization and cross-app hyperlinking has no real negative effects.
The reverse is also true; 95% of the use cases of disparate apps can be covered by a single app and your filesystem. You can keep your notes, journal, todo list, so on, in Notepad. nano for those who use Linux. I mean, why not? Use your filesystem to navigate things, and shortcuts to things that don't fit neatly in a category.
Do you really need Todoist to do what you can do in a plaintext file?
Now, this isn't an attempt to mock the OP. I don't disagree with most of the points they are trying to make. But most of the premises, while well thought out, are a bit flawed.
> long-form study notes are a form of procrastination.
It's the first step to taking notes. You need to distill them into chunks that you can review for later. It's rarely meant to be kept in its initial form.
> Contacts: if you have a page for a person ... use Google Contacts or a spreadsheet.
Or a text file with their name.
> Fiction Writing ... using git for version control makes a lot more sense ...
A git folder with text files.
> Organizing Legal Documents ... a few spreadsheets is all it takes in practice.
Or a folder with PDFs.
> Lists: of things ... Spreadsheets work just fine for this ...
A collection of text files is fine.
> Collection Management: this is an area where the software solutions are strangely very lacking. ...
Nope, text files.
> I need tags, that is: I need a database.
Ah, that's what OP wants. A database to Do All the Things. Seems like OP just wants a better Excel. Sorry, my cynicism was showing.
(as for Collection Management, why not a spreadsheet? It's the same problem).
I use Obsidian, and before that, I use Emacs, VimWiki, LogSeq, Roam, Dendron, etc. I find it fun - it's a hobby of mine. What I find fascinating is the myriad of ways people have come up to solve this problem, and of course, this problem space has no end of salesman.
At the end of the day, I find Obsidian as a "pretty text editor with a really fast search" useful currently. I keep my tasks in there, because 95% of my "tasks" are just text files. I leverage a plugin (Tasks) to let me sort it by date and one that lets me put it anywhere I want. (So I don't have to figure out where it belongs)
> but a nicer UI ... the UI trumps the features ... is about building a habit, for which good UX is necessary.
Exactly. Obsidian themes have a pretty UX and the plugins make plain-text a nicer UX. Tomorrow, I might switch to LibreOffice because, why not?
I use the filesystem for everything else, and for things that don't fit neatly in a category? Hard links, if it makes sense. I find that trying to collect everything and organize everything is a rabbit hole in and of itself.
It's the same problem that hoarders have in meatspace , and rich people solve by buying bigger places.