Here’s a way to think about this: Web Annotation is totally cool, W3C media fragments finally put to some better use and standardizing the semantics. Hypothes.is doing all the work is a great contribution, but on the other hand, very unhealthy to just have them around as the major implementation, also again a very dumb idea to slap Hypothes.is onto Websites, to become dependent on their server/domain, plus it’s simply avoiding the copyright issues, so what’s the point of annotating restrictively licensed material or such that can simply vanish from the Web, and even if you have a local copy, you’re not permitted to share or re-publish, orphaning the annotations. Instead, better add independent Web Annotation implementations everywhere and annotate libre-freely licensed repositories.
Other than that, Ted Nelson has his Edit Decision Lists around for quite some time as well, even with new implementations of sorts in the form of the xanaviewer and span selector.