I can see your point, but the current system works for me
because 95% of the replies are in answer to a Seekers of Perl Wisdom question
(or a Meditation or Perl Monks Discussion like this one) and so they seem to
"belong" with the others. I don't really have strong feelings one way or the
other, however, and I may only prefer the current way due to it always
being that way for me. At the very least, I'd like to keep the
Breaking News and the Q&A sections at the bottom, as they are different
enough from the other sections to warrant it, IMO. Both Tutorials and
Cool Uses are rare enough that moving them would not really
bother me much. My pet peeve is people who change the
title of their replies, so that one cannot tell what thread
it belongs to unless you read all the root nodes and memorize
the titles as you go. True threading on the Newest Nodes page would
make a very nice feature and fix that problem.
my TwoCents;