1. "Comment display is broken". That's a matter of opinion. I personally prefer threaded comments as I find it easier to see the structure of a conversation that way. HN and (sorry) reddit use threaded comments, and I'd consider their comment systems among the best on the Web. Youtube, on the other hand, goes for "flat" comments, and, well, have you ever tried to follow a conversation on there?
Either way, Disqus actually gives the site's administrator the option: http://whatever.disqus.com/admin/settings/appearance/. The author is right though, having the ability to switch between the two on the front-end would be super.
2. "Comment paging is broken". Completely agreed on the 900+ comments on pages of 10. However Disqus gives the administrator the option to separate comments into pages or keep them all on one page. I personally don't get hundreds of comments, so I keep pagination turned off.
3. "Login kills comments". Sounds annoying, but honestly that sounds like user error. Disqus does say "Post as..." when you're logged out, which I guess is KIND OF ambiguous, but surely it's the user's responsibility to make sure they're logged in under the correct account if that's what they want?
4. "Newest first is weird". Why? I prefer it. Again, personal preference. And again, Disqus gives the site administrator options for sorting.
I don't want to sound negative, but I can't help but feel this post was ill-thought-out and badly researched. The sites the author is speaking about have apparently just switched to Disqus, so I'm going to assume the administrators haven't got to grips with how the service works yet.
Finally: I just realised that I sound like a PR stooge for Disqus. I'm just a user, honestly.