Am always impressed when a freemium plugin works so well. It does make one seriously consider upgrading to pro!
Suggestion: Without morphing in to a document management plugin, there are a couple of other file managment plugins that offer "sync to folder" capability and that directory can sit on the server, S3 or Dropbox.
I know this would materially alter the management-per-file aspect of your product, but would be useful for those organizations we work with who deal with lots and lots of files (with varying permissions).
Great job on this and, by the way, very tight coding (which is impressive).