I don't think there's a one-sized-fits-all solution. Tree comments do solve many issues with linear threads, but they do introduce their own issues, especially when paired with voting. Many cases do work better for tree-style comments, but there are cases that work better for linear threads.
But it sure fixed some of the more infuriating aspects of classic / linear forums:
- long (winded) conversations between posters in threads
- off-topic discussions / people de-railing the threads
- finding things from specific dates in very large threads.
Some of those things are easily fixed with very active moderation - but self-moderation (via voting) sure works fine in most cases.