The hierarchical threading had been one interesting feature, but was itself prone to quickly become as confusing as the stream mode: The indenting of each and every reply made for long strings one had to scrutinize carefully in order to find the dent the reply replied to. Helpful in short conversations but confusing in larger ones. (A combination of both might actually help ease the problem, putting notes into a stream line as long as there is no further reply indenting the conv to the right).
But a main conundrum for GNU Social is: In implementing more and more the features people are accustomed to on Twitter, the less it becomes reasonable to leave Twitter for GNU Social. This could only be avoided if GNU Social would come up w/ a good solution for displaying conversations -- something that hasn't been achieved by Twitter or Free Media.