You're obviously not paying attention then. Plenty of people have posted *exactly* what's wrong with the comment system in beta. Maybe you haven't seen them because you're actually using beta?
Look, you have to understand something: Slashdot discussions generate interesting content by allowing tons of garbage to be posted, mixed around, and evolved. Part of the evolution comes from the interactive nature of community discussion, and part of it comes from the moderation process. For this evolution process to work properly, you have to be able to see a lot of posts at once, all in one shot. You need to be able to see some contextual information about the people posting comments. When you post your own comments, you need to be able to quote or link to other posts easily. When you want to moderate, you need to be able to do it in place, at the comment you intend to moderate.
Beta breaks all of these vital features; without them, the nature of Slashdot discussion changes completely. People will read fewer comments because the new layout hinders rapid seeking, scanning, and comprehension of potentially valuable posts... all while making it much more difficult to skim past the stuff that doesn't interest you. When people read fewer comments, they post fewer comments. When the total number of comments starts to drop, the exploration of the discussion space becomes much less thorough. Potentially valuable or interesting discussion paths will be missed. Those rare, but highly sought after gems of insight and wisdom borne from the cesspool of chaos will become much more scarce.
You want to know why people hate the beta so much? It's because it kills the evolutionary discussion dynamic that makes this community what it is. There's nothing else like it, and many of us do not want to lose it.