I think people try to do too much with note apps and then they fail. What people normally try to accomplish with a note app should actually be like 4 - 5 different apps which handle different elements of what you're trying to accomplish with notes.
Or at least, it would be 4 - 5 completely different processes and a given note app isn't best for all of them.
I use...
App for capture and inbox (this is an actual note taking app but I don't use it for writing)
App for writing notes (my own writing
App for display and management of networked notes
App for arranging (networked notes), outlining and building to the draft stage of writing
These are all part of a typical note cycle which many people use one app for. I put these notes through a cycle in the order that I wrote them. Typically I would start out with capturing information, then creating my own notes from that information and then eventually using that information for my own writing. I'm not a writer, but writing helps me think through things I want to understand better.
I could constrain myself to a physical journal. I could constrain myself to anything. It would drive me nuts though. I would end up attacking the journal with scissors and then pasting pieces of paper to the walls. Then arranging pieces and pasting notes on top of each other as my ideas change.