How can they make a mistake like this? Unless they are aiming to change how people comment on things. That won't happen without an interface change IMO because people are used to the way it was for about 4-5 years..
Well, they needed to do something about the comments on really large pages, because those were useless before: you'd see a disconnected selection of the 25 most recent comments and a link "2864 comments, click here to show 25 more". Those people were only sort of / sometimes responding to each other, and even when they were the comments all had tunnel-vision on the most recent 25. Even just showing "comments on this massive post made by your friends" would be an epic improvement (and something it seems they are now both able to do and are actually doing), but that already breaks chronology even without "bubbling".