Encouraging selective quoting with interspersed comments, but having seen the triumph of top quoting in e-mail discussions, this might be a lost art anyway.
Also, personal kill files. Bring back the PLONK! Thanks to the thread organization of HN, subject kill files are no longer really necessary, but being able to mute people for 30 days or permanently may still be useful (And it might contribute to downvotes being used less for subjective differences of opinion).
I also used to like the ability to easily take discussions to email, but Usenet was a smaller place back then and this may no longer scale.
If I cared I could dive down and see where conversations were happening. as it is I really only spot a top couple.
I guess it's halfway between real state and ephemeral
A modern example of this is lambda-the-ultimate.org, which has so many threads that have been running for years without any clear purpose that it's almost impossible to find a thread that hasn't.
Of course, that could be a matter of scale; with less posts to keep track of, I guess it would be easier to continue things eternally.
Looking at HN discussions today it has very few of these, in fact you hardly every see the parent counter-replying to someone opposing his argument. Instead often others reply with a different perspective or the discussion dies because why argue with a troll. Maybe even the lack of quoting is a big contributor to the healthy discussions here.
Branch pruning, a la trn (threaded read news). Allows one to tune out unproductive flamewars. Kinda goes hand-in-hand with facilitating long-running threads.
Some version of killfiles, but somehow magically adjusted for a world in which trolls can make new accounts easily.
Or expanded ones, if I came into the topic w/all nodes collapsed.