Let me ask you a question: if we'd spent a bit more time polishing the site and then just set it live for 100% of users, do you think that would have gone better?
You do know that that wasn't the only other alternative, right? Looking back, might it not have been better to post a message *before* you started redirecting a sizable section of the traffic that said, "we appreciate the feedback we've been getting on the beta site, and we're working on implementing many of the changes that have been requested. We know that that there are still issues with several components of the site, but in order to get feedback from a larger sample size, we're going to redirect 20% of the users to the beta site as a trial for the next N weeks. After that trial is over, we'll go back to classic Slashdot while we continue improving our new design." It's called managing expectations, and would have had the added benefit of giving people a place to put the Beta protests.
Also, you keep saying that the comment system is being worked on, but your "Beta News" section doesn't list it under "what is not in Beta yet" as one of the "key areas being worked on." So, it's perhaps natural for people to assume that you're not currently as concerned about its problems.