Oh, I see I think I misunderstood your question. HN has points, and it's more of a two way "discussion." Maybe you should, rather than have comments have discussions (I know this is probably the same thing given a different name)

As for the second problem, I guess (personally) I see a huge textbox where you ask for my name, email and an optional website, and I just don't feel motivated. I think you could have a small, anonymous comment spot that felt more like a tweet rather than a post.

Oh and as an aside, I didn't realize that you had the comment overlay button when I viewed a site. Maybe add some words to the icon to make it OBVIOUS for unobservant people like me?