The problem occurs when you start reading into a nested thread of comments. Users will sometimes argue 4 or 5 times back and forth, often becoming mean and uncivil. What results is a somewhat personal discussion among a few people that doesn't fit in with the rest of the thread. While the quality may actually increase the deeper you go into a thread, the relevancy to the original thread decreases (which matters most).
I think that this behavior is what is hurting HN's overall quality. Uncivil and deeply nested threads like these are hard to keep track of and deeply get out of control.
The solution:
- hide deeply nested threads (greater than 3 or 4 comments deep) and
let the users choose to show them
- promote commenting in higher threads (this will come as a result
of hiding deeply nested threads)
- hide or lessen the visibility of threads consisting of comments
from only 2 or 3 people