If you find a post that starts interesting conversation you can select it as root (or simply double click) and you will get that conversation - all replies and their children, grandchildren etc. So I don't think there is a real need to have tree style comments as the approach to this is different.
Reply system with ability to select conversations is one of the main differentiators from other similar sites. I know people might find it uncomfortable in the beginning simply because it's unusual but I think it's superior system to upvotes/tree style.