I think Disqus also just has a lot of UI issues. For sites that I visit which used to implement their own comment system and switched, it has only been for the worse. You could argue that the opposite should be true since comments are Disqus's job and they can focus on doing just that thing well. But sites where people regularly comment are communities. Each wants things to work a little differently to match how the community functions. But besides that there are more basic things it simply doesn't handle well like paging and collapsing.
