Ideally, what you'd have is something akin to Slashdot, where users can configure the comments display to their liking. I don't know if you're familiar with it, but if not, play around with it a bit. Here's a story currently on the front page. Underneath the story itself, you'll see a couple of drop-down boxes, one of which should read "threaded" - that's the default mode. You can scroll down the story to see what it looks like. Then pull down the box and select "flat", and hit the change button - what you'll get is a flat, chrono-ordered thread, like what FR has. And then select "nested" and hit "change" to see the nested display, where replies to posts are indented to preserve the relationship between a post and its replies, and the replies to the replies.
And you can choose your preferred layout in the settings, and have all threads come up that way. That strikes me as a good idea, such that people who like it the way it is now can keep it that way, and people like me who like a little more organization - not that you'd know it from my desk ;) - can view it some other way.