I'd agree that sometimes the comments don't work - that's why we let you control which sources you want to display.

Regarding replies to comments: I'm not too concerned. People who write entire articles often don't see the responding conversation that happens on Hacker News. Conversations are fragmenting. Lots of people use plugins to pull in tweets and FriendFeed comments, so we thought we could give them all in one.

Regarding grouping: We have an option to push all the comments to the end of the comment section, but we don't group them distinctly right now. We want to do that in our next release.

Thanks for the feedback!