Once it would be possible to store annotations locally in the workspace, I would like to be able to "reply" to annotations already made. This way, just versioning the whole project would enable anybody collaborating on it to add annotations on top of the existing one without altering the original, much like replies. Being able to do so I like a dream for me which is working on scientific documents !
PS: Keeping track of the date of last edit for each annotation would be great !