Well during last year's W3C meeting on the subject, annotation was a form of collaboration. Annotation is not necesarily shared.
Private annotations have some value external to the more general issues of collaboration.
I think in the original discussion, annotations were viewed as commentary on content not owned or controlled by the annotator. The technical issues I see are the correlation between arbitrary content in all its various complex forms. Once the annotation is created in the context of a collaboration support system, I would expect a bit more structure and control which would leave annotations as just one form of collaborative comment which should have the full power of the Collab system to support general discussion. Of course, since we are at the instant talking about a web deployed collaboration support system, it could also be the target of annotations of arbitrary material. I believe this one way connection to arbitrary material is what distinguishes annotations from general discussion.