I'm all for modernizing UIs. Any UI that sits stagnant for an extended period can drift into a case where while it is much beloved, it is not as nice as it could be with some newer thought/style applied to it.
However, when the replacement UI does not keep, at it's core, the essence of what made the former UI so popular, one encounters significant resistance.
Many here will tell you that what makes Slashdot a part of their daily lives is not the articles. Sure the articles are topic starters and they contain some good information in many cases. But the reason many of us read Slashdot every day is that it is made up of a body of commentators who add the actual value of the website. Regardless of what the article may be, or how mundane or sensational the headline is, I have a clear "wait and see" response to it all until I've seen what the Slashdot community has made of the topic. I know that this crowd will dig into topics, look up facts, even unattractive ones, and find the interesting layers that are never part of the original articles.
Articles are the START of a conversation. The herd of intelligent, resourceful, knowledgeable detectives who live here are the actual product that I'm here to consume. I am THEIR audience, not Slashdot's.
All that being said, any changes that take away from my ability to easily consume the comments here is a step in the wrong direction. The new comments system for me is a complete non-starter. It lacks the view of the thread as the thread organically grows. It lacks the ability to see high rated comments inline while still seeing their position within the overall discussion without turning on everything. In short, it makes it harder to do what I'm here to do.
The rest is all window dressing to me. Bigger pictures, cleaner fonts and such. Yes, these things can be great when done well. I'm not suggesting that what we have in the beta is "done well" but rather that it could be done well if you scrap what you have and start over with a new focus on "what is our product" and realize that the answer is "our commenters".
Given the backlash that Slashdot is experiencing, my suggestion would be this:
Announce that you are cancelling the current beta and going back to the drawing board with a renewed focus on the site's content and purpose.
Make it clear that you do not believe that Slashdot is not "just another news site and should be formatted as such".
Show some appreciation for the legendary comment system that Slashdot has grown over the years and a dedication to remain faithful to it.
Then you can start over, and instead of going for a grand redesign, take an iterative approach. Small moves, in alignment with the community.
In the end, your readers are different than any other website news service, they know more about site design and site construction than you do. So tap into that and stop treating them like they are reading Engadget.
Hopefully this feedback helps out.