There should be a different discussion forum which is readable to all but can only be posted in by those with over, say 1000 karma. This solution seems "obvious" as we already have a robust karma system, and it's very difficult to acquire that much karma without actually being a good poster (I don't have that much and I've been here for over a year).
This system could lead to the use of the "open" discussion forum as a kind of training grounds where you prove your individual signal-to-noise ratio and "rationality" is high enough to deserve the right to post in the "exclusive" discussions.
I can already foresee a number of objections to this idea, so I will try to forestall some:
"We already have this, it's called main." Anybody can post in the comments section of a Main article. And the threshold to post to Main is too low in the first place. Have you seen some of the things that make it on there?
"We'll get a reputation as being snooty and intellectually insular!" We already have that reputation, and in any case, it is better to be thought arrogant while having high-quality discourse than it is to be thought humble while having mediocre discussions.
"This would be repellent or confusing to newcomers." I'd argue it's really no worse than the current two-forum system with the current karma system. And I thought part of the point was to put up a filter so we bring in the right newcomers?
(An aside: It's pretty hard to write up a suggestion like this without the tone coming out arrogant and self-important sounding, so sorry about that.)
Alternately: a (very low) karma requirement for comments and posts to the discussion subreddit (~20?), a somewhat higher karma requirement for comments and posts to Main (~200?), and a newbie subreddit for new posters to post in. Regular newbie forum topics would be welcome threads and stupid question threads; anybody could post in the newbie forum, so there would responses from LW veterans, and anybody would still be able to ask Stupid Questions. (Meetup threads possibly should go there too.) (Depending on how many other topics there are, it might be worthwhile for every introduction, meetup, and question to get its own thread there.)
The recent implementation of a -5 karma penalty for replying to comments that are at -3 or below has clearly met with some disagreement and controversy. See http://lesswrong.com/r/discussion/lw/eb9/meta_karma_for_last_30_days/7aon . However, at the same time, it seems that Eliezer's observation that trolling and related problems have over time gotten worse here may be correct. It may be that this an inevitable consequence of growth, but it may be that it can be handled or reduced with some solution or set of solutions. I'm starting this discussion thread for people to propose possible solutions. To minimize anchoring bias and related problems, I'm not going to include my ideas in this header but in a comment below. People should think about the problem before reading proposed solutions (again to minimize anchoring issues).