I've long felt that annotation was one of the greatest missed opportunities of the web. Every major content website implements commenting differently and often poorly. I'd much prefer to have comments come from a third party system where I can: own my own comments, not be subject to removal by the author of the content, and choose the group of people I want to discuss with. Imagine if hackernews discussions appeared…
Before changing HTML link semantics though, HTML should really consider allowing placing href on any element rather than using the dedicated element though (with the expectation that this acts equivalently to an anchor link), like MathML does. In general, I'm not sure hosting discussions on third-party aggregators such as discus.com is really a win for privacy, though.