I mostly agree with Michael, but I think one of the benefits of this sort of view for busy sites is the ability to have a slashdot-like view that shows only a certain depth of replies.
While it's true that people need to be discipled about where they reply, it also allows a sub-topic to become it's own thread if there's enough interest. There could even be UI to allow a thread to be "front-paged" to use a perlmonks-ism.
I have to say though, that one of the things that endeared me to Phil's site and arsdigita.com was the flat time-linear comment and forum layout. I still find it one of the best styles, and it takes a huge volume (like slash dot) for a threaded style to beat it in my opinion.
