Here's another possible but related solution. Have two views, and have a control on the page that will swap between chronological and thread views. In chronological view, have vertical lines behind the messages that connect a message back to the parent message - if it was a response. Don't indent messages - I still want to see my messages on the right and everyone elses on the left. In the threaded view a) reorders messages, b) moves these lines to the left and c) indents the messages. Extra points for animating the transition between views.
As for the site, I know that other's likely have different opinions, but here's mine. I had originally viewed the site with a browser with script disabled. It still worked and was a pleasant read. I did observe an empty panel under "The Solution". Later I looked at it on a different machine where the browser had script enabled and found myself annoyed with animations that added no information. But the missing "The Solution" panel was present. I don't know it I'm an outlier, but I find motion to be VERY distracting when I'm reading.
Another complaint - general but I'll highlight this article - is the ratio of words to markup. For this article, the ratio was about 5% - meaning that only 5% of the characters in the html document were displayed to me the user. That is a very heavy overhead of markup. Is that just par for the course in modern web publishing?