My opinion on threaded replies themselves
It's a good idea on paper, it's true that comments are often heavily disorganised, often by an OP trying to reply to other comments one by one, and comment posters replying too in a different order, resulting in a very spaghetti-ish comment section.
But, I feel like they should display the way YouTube does it, with a max depth of one.
This way, if someone comments, replies to this specific comment will be padded to the right a little and put underneath it, but if people keep replying to each other, you're not gonna get a diagonal line of comments.
About the way threaded replies were introduced without taking any previous feedback into account
It feels like you are ignoring the community a lot, here.
Namely, three of the most important (in my opinion) problems weren't fixed.
Comments STILL take a huge ton of space
Markdown is STILL lost when editing, even though it's been reported three weeks ago and is a massive problem. (EDIT: finally fixed, an astounding 22 days after being reported!)
The comment entry form is STILL above comments instead of below, which is made worse by the introduction of replies:
This is the bottom of the comment question and there are 8 more comments above, and considering how much space they take, this makes the comment second take approximately two screens.
Let's say I, a new user, want to post a new comment, not replying specifically to anyone, just wanting to ask OP for clarification. What do you think I will do?
A. Scroll up to find the "Add a comment" form because I remember it was there, and as a new user, I made sure to carefully read how comments work and am not going to assume they work the same way as on other popular websites
B. Just click the nearest "Reply" button
I'll let you guess which one is the most likely.
It's been 24 days since the initial post, and almost none of the feedback has been addressed. Only three (1, 2, 3a/3b) bugs have been fixed (some of them, silently), and only so because they essentially prevented the experiment from working.
This is a major problem. You can't just move on with the second step of the experiment in these conditions and expect positive feedback.

