[arugulum]

Personally, I don't like using the built-in PDF reader. Its annotations are in a proprietary format and aren't reflected in the PDF itself (which is how Zotero can keep track of them, because they're in its own format). That may work for some users/use-cases, but I like annotations to the PDF to be burned into the PDF, in case I'm using other programs as well. (I know you can export the PDF, but that's a whole other step).

Admittedly, the upside of using the built-in PDF reader is that you can have a seamless experience between desktop and mobile. But the reader itself doesn't have all the features I need.

Personally, I use Zotero + PDFExpert. The killer feature being to crop (desktop) or auto-crop (iPad) PDFs of papers, which often have an obscene amount of whitespace.

The nice thing about Zotero is that it's open enough to support both of our usage habits.