I think you want the right tool for the job, and depending on parameters of the discussion, either tree or flat might be appropriate.
For example:
- Want to “encourage” posts to stay on topic - flat
- Want to emulate an interesting dinner party, where discussions inevitably devolve into half a dozen separate sub-discussions - tree
- Want to keep replies to less than 200? - flat
- Want to encourage participation from as many as possible - tree
- Want to make it easy for casual/marginally interested browsers - flat
etc., etc.
Hence I like flat (Stack Overflow is a very nice model) for technical discussions, tree for political discussions, etc.