Replies listed out of order
AFAIK the site has always, or at least for a very long time, given users the ability to select an ordering for the replies. Nodes that were written to expect a certain ordering of nodes at the same level ("see the reply above/below"), and replies that were not posted as such, are the issue, not the site's ordering of nodes. And I think "best first" is a good default ordering of nodes.
a previous reply which has been suppressed
If you are referring to RFC: Hide Very Bad Answers From Visitors, then see that thread for the reasoning behind this new feature, which I fully support. The "bad" nodes are hidden such that casual visitors and search engines can't see them right away, but as soon as one logs in, they are visible, plus any direct links to such nodes should still work.