Aye. Like Rose, I don’t trust the layers most of these apps add on. I do my annotations in PDF Expert or DEVONthink, maintain the PDFs in the file system, and then use tools like Skim to automate and interact with my notes. So far it’s working.
I recently got fed up with Zotero’s non-native feel, though, and switched to Bookends. Still getting used to it—importing new finds from the web is particularly counterintuitive compared to the magic button most other reference managers provide—but it’s otherwise really slick.