Thank you, tye, well said. Just to add on that a bit....

There is at least one good case I can think of for preferring to have replies ordered chronologically: it makes it much easier (in fact, I'd say it almost makes the difference between possible and nearly impossible) to do a "diff", in your head, of the thread upon subsequent visits to the page. You know that the new ones are to be found at the bottom (at least, for any given branch and level of the tree). I suspect this isn't a common scenario for visitors and newbies; but for old-timers like us, we can easily set that preference in our User Settings. In fact, the "Newest First" setting is probably there for those folks who are so interested in "what's new" that they don't want to be bothered with jumping to the bottom of the page. But if one only visits a given thread once, having the replies ordered chronologically gives no benefit that I can think of.