My biggest complaint is getting content out of Paper. We love it at Wildbit and it’s a joy to use when collaborating with others. The only issue we use it as a temporary space for our documents.
Meeting notes and project plans are fine, but the experience is a little more frustrating when working on a blog post or email newsletter. That content has to live somewhere else (Craft, Mailchimp, Campaign Monitor etc.) and getting into those other tools can be a pain. Copying and pasting does not work well because of Paper’s underlying markup.
But the service is so well done that I’m confident this aspect will improve with time.