Also, there are many innovations in comment systems. Gawker's Kinja system is quite good at surfacing or organizing interesting comments, among other things. Post segmentation and comment filtering are techniques used by Slashdot and Reddit, which dampen the impact of growth on community "feel". But, despite the massive growth, there is strong aversion to incorporating any deep changes here.
I perceive two specific challenges: prominent voices might actually want a feeling that is (or appears to be) impossible to restore, and there's general apprehension about messing too much with the magic formula that brought HN to the point it's at today. With the influx of users, this appears to create an identity crisis for the site.
I wish I could suggest solutions along with these observations.
Edit: I do think it would be useful to understand what members of varying karma levels subjectively/qualitatively perceive to be the values and valuable traits of the site.