There are at least four glaring problems with how you've redesigned the comments:
1) You're wasting at least 33% of the usable screen space for comments. I understand you need to put in some ads but after that you should be using the entire screen to display comments. The new format is hard to read and actively penalizes longer and better formatted comments. Like other posters have said: I come here for the discussions, not the stories, and this is a major turn off.
2) You've dropped the visual cues as to how far down in the thread you are. This is particularly bad in long threads because as it is designed today when I spot a flame war I can pretty easily visually skim past it to the next relevant comment. I can't do that in the new format.
3) You moved 'load more/all comments' to the end of the comments! WTF! I don't want to read down to the end of the screen, load more comments, and then have to go back to the top and try to figure out what's new. Now, you're saying to yourselves: yeah that's not how it works. Now we just add more comments onto the bottom which brings me to problem four:
4) You've removed the ability to filter on moderation rating in the story. It looks like now you're just barfing out the first X comments, regardless of moderation, and the loading X more when I hit the button. I understand how this makes #3 simpler but it's a pain the ass if on one story I want to follow the high level threads and the next I want to read at -1 so I can moderate.
Additionally: I'm really concerned that every comment has a moderate link. Be really careful here. /.'s moderation has warts but it's far and away better than any other moderation system out there. Break this and you break /.
Also on the user page you took away the ability for me see how my comments got moderated (vanity) and also to track replies to comments that I've made (breaking current functionality).
Comparing current to Beta it also looks like you increased the size of the ads. I don't like it but I can live with it.
Overall, this is much much worse.