HN user
We freely admit that there have been many people who've tried to do this, but, to answer your question: Annotator is more granular than Sidewiki (you annotate specific passages within the page), and unlike Reframeit and Highlighter works across the web rather with no requirement for the developers of those sites to have enabled it.
I'm not so sure. I don't think success (whatever that is) depends on a critical mass. In particular, while AnnotateIt has a bookmarklet (and soon browser plugin) use case, it's also possible for it to be useful to individual sites who can use AnnotateIt in the same way that they currently use Disqus.
To address your second point --- well, yes, that's kind of the point. Not to piss people off, of course, but to provide a commentary layer that doesn't necessarily require the consent of the site owners. I don't think that should be seen as a downside of the software.
"Have you considered creating a bit of javascript that any site can embed on their site that would allow a visitor to annotate?"
Yes, we have. It's there on the front page if you scroll down! http://annotateit.org/#develop
"Also, have you considered making it anonymous to start like github:gist?"
Well, you can certainly try out Annotator using the demo at http://okfnlabs.org/annotator/demo/
Just a brief note to say I totally agree! There's a long list of people who've built similar things and failed.
There are two really tough problems in web annotation: 1) changing content and 2) reputation. I freely confess that Annotator/AnnotateIt address neither of these major issues satisfactorily, but work is already underway on problem 1 (assisted greatly by http://mementoweb.org), and we're working closely with http://hypothes.is/ who have assembled the world's experts to attack problem 2.
In short, we're aware of the history, but we think this is an idea whose time has come.