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I am a big fan of the threaded structure because it is self organizing and allows many more people to participate. It also encourages the shy posters, who have much to contribute, to speak up in corner conversations and gain valuable experience. It can be intimidating to demand the floor.
I think about it like a party. Every good party has many different sub conversations, but there are always a few people that can pull disparate conversations together by pure will. Streams that connect to rivers that diverge again.
Your point about community is a very good one. User ranking of posts can help highlight good posts, but also can encourage inbreeding and retribution.
Ultimately, single thread discussions can only scale so far. A pond can only hold so many turtles. The limits of food and living space keep new turtles out and old ones seeking new ponds. Threaded discussions are a way to make the pond deeper.
While a threaded system does not discourage insults, it does encourage complements.