Is there some benefit to making users scroll through every single comment? Reddit has this feature by default. I use a GreaseMonkey script that adds the functionality to HN, and when I browse from another device, I'm reminded how tedious it is to scroll through a long comment thread just to get to the next root comment.
I use the greasemonkey script Hacker News Threadify and it works great for FF:<p><a href="http://userscripts.org/scripts/show/110317" rel="nofollow">http://userscripts.org/scripts/show/110317</a>
Try <a href="http://hn.premii.com/" rel="nofollow">http://hn.premii.com/</a>.<p>Clicking a comment lets you collapse it or the entire thread it's in.<p>Works great on mobile too, feels like a native app.