I find that paradoxically, the biggest problem with Hacker News right now is the hot algorithm we use. It's great for bringing good stories to the attention of the community and having a burst of short lived discussion over those stories, and then dying out. What it's not great for is long term discussions.
For example, with Quora, when someone answers a question, or posts a comment, you never care how long ago it was posted, because there are notifications, and the front page is based on what you follow, not how popular the questions are.
This is a hard problem to fix, but a couple suggestions I have are to improve the threads feature, such that it resembles a real notification bar. Secondly, I think a new page should help, a mixture between the front page, and the saved stories, which shows active discussions, and an emphasis on one's that you have upvoted.
I think those might help reduce the ephemerality of the discussions here.