Comments, and the links they comment on, are different things, so we should not be surprised if the best solutions for ranking them are different.
There is already precedent for treating them differently --- it is possible to downvote a comment, but impossible to downvote a link.
Speaking about that, do you know when that gets enabled? I was thinking it'd happen when I reached 100 karma, but I'm at 131 and still can't downvote. I'm not particularly worried about it...but am curious.
Can you elaborate why comments and stories are 2 different things? I think stories are just like comments but presented in different websites.
Maybe HN should allow users to downvote stories as well? Since some are complaining about their quality.
Stories are usually more considered (yes, I know people link to tweets sometimes, personally I find that tiresome). They make their own context and are often (mostly?) written by people who haven't heard of HN.
Also, I think you misunderstand my usage of a "ranking system" --- it includes not only the method of crunching the numbers, but also the way the votes are solicited.