Yes, I think we'll continue to avoid the notification system, not just because of flamewars but also because (relatedly) it's not so compatible with curiosity. Push notifications seem to jack up the nervous system in a way that's good for engagement but not necessarily for users—we all experience this elsewhere on the internet, and on HN we're in the blessed position of not needing to juice the numbers.
On the other hand, it can be hard to discover replies, and certainly new/interesting comments in large threads, when you want them. I'm currently working on a new-comment-highlighter (draws a colored bar to the left of comments since you last viewed the page) as one step toward helping with this. If anyone wants to help test this, email hn@ycombinator.com and I'll switch it on for you.
