Perhaps my use case is unique. I have to chosen to manage about a half dozen separate citation libraries to work across as many different individual projects and team members. Everyone else uses Windows.
I am staying with Bookends. It offers the best all-around support for AppleScript, multiple libraries with their own attachments sub-folders (no other app appears to offer this), iPad annotation toolset (the Highlights app on the iPad is cumbersome by comparison), and integration with DevonThink.
I’ve dropped Papers. It is professional and very well-designed. I could use it for its ability to search for comparable articles. But this is not my primary need, and its limitations in other areas leave me stranded.
I use Mendeley solely to share PDFs with members of my research team.
I just completed a proof of concept test for how my workflow will run going forward on my projects. A team member marked three journal articles in Mendeley for me to review. I exported the PDFs from Mendeley to an > inbox folder at the Finder level. This folder was set as a Watch folder for a certain library in Bookends. When I open that library in Bookends, it imported the PDFs, completed all the meta-content, and moved the references to a Static Group called > to review. I synced only that category to Bookends on my iPad. I pulled up each PDF, annotated for highlights such as #why, #how, #result, and so on. I synced back to Bookends on my computer. I exported the annotated PDFs into a Finder folder > to Mendeley. I replaced the PDFs in Mendeley with the newly annotated files. The most difficult step in this was the last one. Mendeley is not well designed to swap out PDFs with any degree of ease. The biggest frustration in all of this is that Mendeley does not recognize any form of annotation or note from external apps. I tried annotating in Acrobat … Mendeley does not recognize it. Yes, you can see the annotation on the PDF. But you cannot see it in the notes list.
Otherwise, I’ve tried but not taken to Zotero. I get lost trying to set it up properly for citation management. I hear all the great things about Zotfile or the annotation options on the new iPad version. But … setting up Zotero and understanding how to get it to work always seems to cause me more friction compared to working with Bookends. I keep Zotero if only as an option to replace Mendeley for sharing in case one or the other of my team member prefers.
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JJW