Threaded comments are a bad thing. I've gone through this thoroughly in a blog post (http://blog.iroquote.com/post/45908133231/5-reasons-why-thre...), but here is an overview of why:

1. Screen width limits the depth of threaded replies.

2. Indented replies look horrible on mobile screens, and make the depth of reason (1) even smaller.

3. We (typically) lose chronological order.

4. A complex comment tree makes it cumbersome to track who replied to what.

5. Non-techy users don't get it well, which eventually leads to a inconsistent tree.

I think the search for an ideal comment system is a problem worth solving. IMO it is best solved by:

1. A single thread in chronological order.

2. Quote feature, like in forums, to allow direct replies.

3. Some summarization technique to highlight relevant comments.

That's what I'm doing at my startup, and I would like to see other approaches too, because it's about time we figure out how to do an intuitive and powerful comment system.