This is precisely the problem. Without some idea of what earlier readers think of the comments it is much harder to skim.
The top-level comments presumably rise and sink based roughly on their karma (though the algorithm also seems to have other considerations, like momentum). But what of the second-tier comments and below? Ripostes are often where the action is.
I might find that I'm reduced to skimming for names that I recognize. That's how the rest of the web works. The web in general has no karma system, so the way to "upvote" something is to repeat it with your byline: You Twitter it or reblog it (or retweet it, or re-reblog it) with a link and your signature, implying a certain degree of implicit endorsement.
I expect that if this system holds we'll start seeing more "amen" comments. I kind of hope so, frankly: Now the only way I will spot an incredibly insightful but short comment buried downthread is if I see a bunch of comments from people I vaguely know saying "amen".
I'm not sure this trend will represent progress, however.
If we want to tinker, consider this: relative rankings on a page. Find a way to distinguish the top-voted 20% of comments from the second quintile, and the second quintile from everything else. (My instinct is not to bother distinguishing things below the top 40%, and of course negative-karma comments presumably are still doing their disappearing act, my favorite cute HN feature.)
At the risk of repeating the legendary eye-searing Orange Name experiment... we could turn the byline of comments in the top 20% a different color from the second 20%, which in turn is a different color from everything else.
Red is probably the wrong color for any of this -- too loud. Think "green". I'm thinking shades of green: Comments in the first quintile have very green bylines, comments in the second quintile have slightly green bylines, and all the other comments have their usual light grey bylines.