The problem of unintuitiveness is sadly very common in Free software, but it's getting better... in a few spaces anyway.
For an Apple Notes replacement, I would suggest looking at Joplin, which I use daily for everything from database diagrams to recipes. It has a built-in sync feature, supporting a variety of options, all encrypted. I used it with Syncthing, which admittedly isn't very easy, but there are other simpler options.