In terms of moderation, a note on when/why threads were moderated would be nice. Sometimes huge chunks of posts or whole threads disappear. Usually it is obvious why, but sometimes it would be nice (and establish the tone for the site) if reasoning were supplied. It is also frustrating as I think in at least some instances people spent a lot of time on useful content that was only tangentially related to some flame fest had their entire post removed. That doesn't encourage spending time on future posts.
The hows and whys of moderation seems to be pretty consistent over the last few years: A thread turns from it's subject into some kind of shouting match, where the subject is abandoned in favor of denigrating the character/intelligence/honesty of the person holding an opposing viewpoint.
The process of untangling this junk posts from those related to the subject at hand is a daunting process, both because of the limited functionality of the moderating tools, and the desire to keep a readable thread that doesn't include responses to posts that have been excised.
It takes more time than I'm able to put in. I certainly see your point about how discouraging that must be to people who've written out thoughtful posts. I confess that I probably haven't given those folks adequate consideration. Faced with carrying threads with 10% thoughtful material and 90% chaff, I've mostly favored hitting the delete key.
In the past, I've tried to keep the forums as inclusive as possible, and that's meant having people with radically different points of view. Moving forward though, you're going to see me insist on a higher level of discourse from folks at the extremes.