I'm attempting to solve this, at least for iOS devices. My technique is to collapse everything first. If you want to continue in that discussion, you tap to expand. I think it helps mitigate the need to comment on the top thread, and should make for more diverse discussion.

I think every platform needs its own interface for this, and I suppose the thought behind the web interface is that you can always just scroll down. It's suboptimal on long threads, though. I found my technique worked best on mobile, since you can quickly tap the entire comment to expand it. With a little JS, this might also work on the web.

(If interested, the app is called Pivit, and is in review -- follow @alariccole if you want to know when it drops in the next few days.)