find a way to present the comment threading more intuitively
Check out https://blog.torproject.org/blog/did-fbi-pay-university-attack-tor-users#comments then scroll down and try to figure out which comment is replying to which comment.
The hierarchy is still basically flat, and you have to count the number of vertical lines to the left of the comment to try to figure out what's going on.
I think it could be improved by indenting comments as a function of where they are in the nested hierarchy.
But that's not the only possible way. I suspect there are other, better, options too.