How do you handle that anyway? If you make it a flat discussion, if someone brings up a new topic (in other words, a branch) then how do you respond to it if there were lots of responses between the time you wanted to reply and the time the original post was made?
If you have a long distance between the original post and the post you are responding to, then that means that the audience loses context and don't know what you are talking about - thus instead of asking "how many people will bother to read past that first massive 50 reply tirade?" you now have to ask "how many people will bother to read past the first insightful comment?"
Basically, how do you keep the thread of discussion without using indenting, or expanding/contracting the discussions? I can well understand that StackExchange needs to keep discussions punchy by design, because it's about keeping information succinct in order to properly answer questions, but on a site like HN that is designed for discussion I think that flat discussions would be an absolute disaster!
Slashdot actually allows for flat discussions, try using it sometime and I think you'll see that it's a nightmare.
