Personally, I don’t need much from this type of software. I read all my PDFs on macOS in Skim, for its inline annotations, which allow me to tag text (using a few tricks I developed long ago). For extensive note-taking, I use BBEdit (I hook the PDF to my BBEdit).
I’ve not written much academic stuff since switching to Bookends. What I mainly want that doesn’t seem to be in Bookends, as @ryanjamurphy metioned, is excellent ability to get the full reference from a PDF. So I’m having a look at Zotero given that Zotero 6 is out and seems to be getting good reviews. I’m also considering (finally) switching to LaTeX after all these years.
I recall @ryanjamurphy published a method to get the best of both worlds (zotero and bookends). But I would prefer avoiding going through that loop time and again if I can. From his comments on Zotero Version 6 Released - Software - MPU Talk, I don’t see an indication that he’s made the jump to Zotero.