climatefeedback.org is a good implementation of Hypothes.is They get scientists to check climate-related articles. Check them out and support them if you can. Good people doing good work.
I know the guys who worked on the W3C spec. They worked their butts off. I'm hopeful they'll have some success. But my system (Fiskkit.com, if curious) can't consume W3C annotations because we have more narrowly constrained parameters to enable analytics. But maybe we'll be able to export in a standard readable format? We'll see. Too broke to build that right now! :-)
I don't think it's unsolvably flawed. It's just hard as hell. If you take a structured data approach to annotation and commenting, you can use analytics to weed the naturally-occurring power law distribution of comments down to just the best ideas on any particular sentence, for example.
Mind reading + ad hominem
You should probably not criticize the quality of other people's critical thinking.