I too have really been enjoying PP because of the Google Docs integration, which for me, trumps any of the other advanced features I'm giving up. That said, the one feature I am really missing from Bookends is the ability to search my notes, highlights and tags. Without this feature, I often have to leave Gdocs and start randomly opening PDFs in PP looking for a highlight that I vaguely remember making. So far, I've resisted the urge to setup a sudo-sync between PDF and Bookends (or other), but I might have to.
Can't help but wish that PP would partner with a mature desktop app such as Bookends. Seems like a better way to expand customer-base rather than trying to compete on every feature. (Then again, I'm no developer, and I don't have insight into PPs business plan.)
Can't wait to see what these new features look like.