Replies to other journals in journals is another thing entirely. From what I've seen, there haven't been many journal wars (like back in the day of the Journal Junkies) lately. Sure a couple of people have posted some angst that has gotten a few replies, but nothing like the craziness back in the day. So this is where my opinion on that comes from.
I do think that the journals could use a comment system if only to keep it all together/better organized. This issue is actually why we have the PM link up there now, so that people wouldn't have to reply in their journal. However I've nothing against public discussion in journals, a comment system might benefit that.
I was getting the idea that people replying to QCs in journals somehow bothers you. As for that situation, my opinion still stands, if I feel like responding to a QC in my journal, then I will, weather or not there is a reply box for QCs.
As for QC's I don't see "anonymous" as "better" because if I don't know who the person is, how can I know if I respect their opinion? I respect the opinions of people who are willing to back it up with their screen name more than people who hide behind being a blank slate.
[Edit] I'm pretty vocal on this, because I used to be heavily involved in the community that was gathering around the journals (which seems to be really dying now). A lot of this discussion has been brought up in the past, and the answer we got back then was "it's too complicated/the coders have lives". There has been a lot of talk about overhauling the entire site, but considering how dead that's gotten, I'm starting to think it's never gonna happen.