Flagging seems like the solution to toxic comments, and should be more encouraged. At the same time, this means it overlaps with downvoting—but only
one use of downvoting. Really, the meaning of downvoting on HN is somewhat confused and muddled: is it a "flag lite"? Is it a way of disagreeing? Is it a way to push worse content to the bottom? Is it just the opposite of an upvote?
Any one of these would be reasonable, but having all at the same time is not great. But that's exactly what we have now, both in the design of the feature and in how it gets used in practice.
Personally, I think downvoting should move away from being an alternate form of flagging (with flagging, perhaps, taking a slightly more prominent role for dealing with actual abuse) and more towards just being the opposite of an upvote. This still makes it a bit of a hybrid (both for moving bad content down and disagreeing), but one that makes a lot more sense because it works just like upvotes do.
For one, this is what the interface already implies. The downvote button looks just like the upvote button upside down. Seeing the two as exact opposites is entirely natural, and that's how it plays out in terms of karma too. But in terms of social conventions and, importantly, greying out comments, this doesn't quite hold.
I also think that some symmetric way to counterbalance upvotes is actually useful in and of itself: downvotes can offset comments that gain a lot of upvotes before getting a strong rebuttal or comments stuck at the top of a discussion because of other quirks in the system. But people now seem pretty hesitant to use them this way. Which makes sense: if downvotes are, in part, mini-flags, they are too strong just to indicate that you think something has been upvoted too much or is not a particularly good comment (without being bad or abusive).
So what would I do? Well, from the site's perspective, the main tweak is greying out comments after more than one downvote. Still have the votes change the order, but only have a really visible effect after a few have accumulated. More importantly, from a social perspective, it would be good to reach consensus on what a downvote actually entails, namely that it's just the opposite of an upvote, neither more nor less.
Disentangling flags and downvotes like this will improve the utility of both features by making them more focused. Downvotes can be a symmetric force in shaping discussion while flags could be pushed a bit more as means of pruning actively harmful comments.