I hear you, and frankly, I think you should go build it. Not only do you sound equipped to do so, but I also genuinely think there’s a real place for the specific blend of features for the comment system you describe.
I suppose where I disagree is in the fact that these aren’t tweaks to News Genius as much as they are platform overhauls. In your passion for UX design, you clearly have this vision for a more perfect comment system, but your redesign might be better suited for another platform (e.g. Medium or Wikipedia?), upon which your suggestions are more of an evolution than a revolution were they to be applied.
For example, you say “It’s focusing the annotation system on its purported mission, which is to hold news companies accountable for what they write”… but that’s your mission; that’s only a subset of annotation’s raison d’être; that’s not even close to News Genius’ purpose. News Genius is more of a platform for discourse than watchdogging…
“Rather than thinking of reporters and news organizations as the gatekeepers of information, we see news as an ongoing and evolving discussion between many parties.”
There’s a lot to unpack in our back & forth here, but that’s the heart of the matter: I don’t disagree with your vision or ideology as much as I disagree with your vehicle (Genius).