Funny, I was just having a real-life conversation in which I was saying that I prefer the Metafilter style and find it difficult to follow HN/Reddit threaded conversations because it's non-trivial to find updates and all the action ends up in the first thread when there might be some good stuff below.

Chowhound has a nice compromise where it's threaded but all the comments you've already seen are folded by default. I'm sure there must be other communities that do the same thing.