I've had a few posts deleted which were "general chatter", but were directed more towards one person. Thats understandable however as it can distract from the topic of the post. But it makes it difficult to continue interesting topics of conversation which are starting to diverge from the post. This is where I think a simple messaging system for the site would be useful, especially given the networking incentives of beginning startup entrepreneurs..
I think there may also be a general reluctance to post things which are challenging or negative for fear of either being downvoted like crazy, or looking bad in the eyes of YC if you have plans to apply. I wouldn't go as far as calling it sucking up, but it could refrain some people from saying whats really on their mind.
The rate of submissions seems to be increasing too, which can make sifting through the new postings more difficult. It also dilutes commenting I've noticed. This could be why major posts like a new PG essay seem to gravitate more discussion. I would personally be game for the idea of limiting the number of new submissions a user can post over a given time. Maybe scale this value based on karma. This would at least make people think more carefully about what they are about to post. I understand this starts to limit the "anyone can post" nature of the site, but it could reap an overall benefit for all users by reducing information overload and concentrating discussion on fewer, good submissions.
But you bring up a good point.. I'll make a conscious effort to post more challenging, thought provoking comments. I've got karma to burn :)