Bear lacks folders. Sure, it has tagging, but it's really a poor man's organization tool; for example, you can't create a new folder and then drag and drop a bunch of notes into it. Changing the "location" of multiple notes requires search and replace, something I don't think Bear even does (at least not the iOS version). Tags also clutter notes visually. Do you put them at the beginning? At the end? Either way you will see the tags. Very strange for an app which boasts about providing "beautiful" notes. There are ergonomic issues; copying a note into another app includes the tags, for example. Selecting a whole note and clicking the "italics" shortcuts will make the tags italics, too. And so on.

Same goes for the Markdown. Maybe some people find Markdown codes scattered all over the place "beautiful", but I don't.

Bear also doesn't handle images very well, at least on iOS (I don't remember how it behaves on the Mac). Images are rendered full width. You can't create nice grids of images like you can with Evernote.