No, it's set that way because I limited the max depth of replies to 3 levels. If you want to reply to someone else now, you'll have to reply to the one that person replied to. ish.
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I'm no particular fan of Wordpress' solution to comments. Sure, it reduced the amount of templates you have to edit to about one or two lines, but it looks horrible. They've reduced the font size so that the threaded comments can be shifted to the left somewhat without having to expand over to the left border or to have very thin text, but imho, doing the whole size reduction sux. I'm more a fan of
this site's comment system. The news article itself is about the same width as ours, but they have a sidebar next to the article with additional information, options, related articles, etc. That wide space is left blank underneath the articles, which allows the comments underneath to have quite some space to shift to the left. I dunno how deep their max depth of replies is, but I can imagine it can be pretty deep, 5 or more levels.