At least for me I hate nested threads. And even worse is when upvoted stuff gets pushed up to the top. On HN I wait to read the comments until there is about 50 of them. Then I never visit the comments on the article again. Maybe there is a way to just read the new comments without digging through the stuff I have already read and I haven't found it. And this is also why I never respond if I make a comment here. It is simply a pain in the ass to find what I wrote again.

But I have no problems on metafilter that is a single (flat) page with sometimes thousands of comments.