First, let’s be clear: Apple Notes is not innovative.
It’s awesome that you like it, but your article is proof. You don’t cite one truly innovative thing about it. The part that makes it better for you is the cloud-driven persistence, which is really just, ahem, the Internet.
A better (for me) and more fully functioning note taker is Workflowy. I’ve been using for years across both desktop and mobile. On mobile it’s an app, and on desktop it’s a Google Chrome App. No saves. Works offline. It’s in the lineage of the 2000's (or earlier) note-taking apps that you describe, but adds hierarchical sorting, hashtags, formatted exporting. I put meeting notes, lists, and to-do’s in there. Say you are in a flight and are reading a bunch of magazines. You find some gadgets and sites that you want to check out later. So I #link and #read some URLs, #nyfood new restaurants, etc. You can move entries into new subcategories just by dragging stuff around, indenting and outdenting to place things in and out of buckets. Try it!
Once you hit a certain number of words, you will have to pay $5 a month, but that for me is well worth it, and a way to support development and storage costs for this excellent service.