I'm implementing Q&A service for my project and I can't really choose: to use linear or hierachical answer comments structure. Hierachical looks more appropriate for me, but linear is much more compact.
See this Meta SO post for a Greasemonkey script to do that.
Because linear comments suck.
This is a Question&Answer site, not a discussion site. Threaded posts are vital for a healthy discussion, linear comments make it impossible to properly follow the flow of a (distributed) discussion. And that's exactly the point: discourage discussion by making it hard to have a discussion.
Another point is about the comments themselves: they are second-class citizens. They only support a subset of the formatting options that other posts do. They have a pretty harsh length restriction. They are rendered in a smaller font.
This creates a divide between the poster and the commenter, which, again, hinders discussion. A healthy discussion requires that all participants be equal.
So, in short: comments are deliberately made this way to discourage discussion, because this is not a discussion site.
Usability. Every additional click, when required to use the application decimates audience of users by factor of 2.
Population of planet is a limited number. After 33 clicks application becomes theoretically unreachable dark matter. We can not prove or disprove that such applications exist, because no evidence was ever obtained.