I think you've hit on a key issue that community size plays a large factor in the quality of discussion. Many of the niche subreddits I visit still have thoughtful dialog. I think any community will suffer an Eternal September effect as they grow more popular. One of the ways reddit avoided this was by allowing new communities to form to mitigate this (see /r/gaming -> /r/games -> /r/VideoGameAnalysis) but I'm not sure if there's any way to completely avoid this fate. Another way some communities have handled this is through strict moderation/curation (e.g. metafilter's cost for signing up, strict moderation of /r/askscience )
I think Hubski's method of following users and being self moderating is an interesting idea, especially combined with the focus on slower, long form material rather than "fast food" content. Though I'm sure there will be some people who will complain that the recent influx of users from reddit (of which I am one) has degraded the quality of content. But hopefully that will not be the case.