My first thought when after reading how many people abandoned the site based solely on the format. There's some excellent, excellent content on there that's worth putting up with a format you don't get on with.
I think the main issue is either people are too stupid to know how threaded conversations work, or aren't old enough or been on the internet long enough to have used them (which would mean they're too stupid since kids can work it out in several minutes). They're not prepared to learn how threaded conversations work, which is their problem, not the site. Or they're simply too cool for school and only ever read OCUK and the Daily Mail.