It is funny, because I agree with your statement. But I never thought of Reddit as made for discussion. Maybe I miss out, but I always have a terrible time following the comments on Reddit (granted I don't even try on Digg and comparing Reddit to HN might be apples to oranges). The comments are usually confusing and non-beneficial to me.
I get great mileage out of this "hide replies to comments" bookmarklet - it allows me to quickly read the best-rated comments that reply directly to the article. If a comment is thought-provoking I'll click through to see what discussion it's spawned.
i know from reading reddit often that there are frequently highly-rated comments as replies that are several levels deep, and possibly have nothing to do with the original top-level reply.
i recommend sorting comments by "best", and then just cranking up your minimum score rating in your preferences so that comments under, say, 10 will not get shown.
Funnier still, I see it the opposite way: reddit discussions are, more often than not, more valuable than the articles themselves (although the s/n ratio is diminishing).
Same is true for HN, but the s/n ratio remains quite high.
