Earlier quoted context omitted.
I was an early EN user from way back in the day when the UI metaphor was basically an infinite roll of paper. I abandoned EN around the time everyone else did for a Dropbox synced folder full of markdown files. I use Sublime Text as my client on the desktop. For my particular use case (I never really used the advanced EN features) it's worked well. I never really created notes on mobile, but I can read them using the…
I am curious how do you handle search? Is that even a use case for you?
I favor the same approach. In my case, I use org-mode instead of markdown as it offers a few niceties when editing from Emacs. But irrespective of that, IMHO plain text overrules any other choice as it is future-proof and can be composed with your favorite tools. For example, a VCS like Git.
I have many files in a flat zettelkasten-like structure [1]. That means, essentially, having one file per concept and using links to chain them.