A fundamental problem of using simple text editors for note taking is you can't easily click-jump from one note to another. If only TextEditor, Notepad, GEdit etc could make clickable hyperlinks whenever they encounter a string which is a name of a file existing in the same directory - then yes, they would be enough. And people who want a graph could just have it as a separate simple app in that case.
I used to think this was quite important and I still like the idea of interlinking notes, particularly for when I am using my phone.
But it is ultimately just more gardening.
I tried all sorts of systems like that and they all disappointed. What really matters is absolutely instantaneous search.
Edit to add: Apple Notes has finally added note-to-note linking, but at the moment I don't have all my Apple devices sufficiently up to date so I haven't tried it.
Notes also has tagging support which is another one of those things I was sure I'd use a lot more than I actually do.
It seems like such a useful feature but in reality I have a few pinned notes for to-do and shopping lists and ideas, and otherwise just make completely unstructured random notes, never using anything but tagging and setting the colors for pinned notes.
I have Calendar for reminders, and markdown files for things anyone else will see. I just need it to work, open really fast, search, and that's mostly it.
By the way, an obvious idea just hit me, taking 2 days like obvious ideas usually do: perhaps a slightly less basic text editor like Notepad++ or Sublime can do a great lightweight yet powerful note taking app if you write an extension for it (or if somebody already has done just that).
But these have another problem Notepad hasn't: they apparently don't support Windows' auto completion. I use Windows at work where I am to type in languages I am not perfectly fluent in so I make heavy use of autocompletion to prevent spelling mistakes.