Paperpile would be the jiggy joint if you improve annotations and note taking. Each notation within a document should be separate not one note as it is in now in Beta. Notes should be searchable as well. Of course, highlighters and tags are important too. Keep us posted.
It sounds like you might not be using our beta viewer. Our beta PDF viewer has searchable notes and highlighters. The main drawback is that the notes are tied to the PDF and are not currently synced with your library, so you will have to open the PDF to read/search them.
You can activate it in the “Browser Integration” tab in the settings menu. Under PDF Viewer select “Viewer with annotations (beta)”.
Now don’t I feel silly. I just assumed when I opened the PDF viewer and saw the words “Paperpile beta” at the top of the page I was already in beta. Thanks for your help Jason. Where can I get instructions on how to use beta?