I really like the fact that you can reply directly to a given comment, but all the "automatic hiding" makes it really hard to find new posts and such.
The other thing I find confusing is that when you reply directly to a comment, it gets "out of order" so when you try to read through the comments to get an idea of what has been said and the flow of the discussion, it sometimes is very difficult. Add to that what Chris mentioned about hidden comments and not being able to find new posts and things get a little confusing at times. Also, sometimes when you post a comment or respond to a question, you realize later that you have duplicated someone elses comment or question. As a habit, I read the comments "top to bottom", so I don't miss anything and I get an idea how the discussion has evolved. I assume that the newest comments are at the bottom of the thread but that is not always the case. And it is frustrating when you get a notification that someone has made a new comment, but when you click on the notification, it doesn't go directly to that new comment. Then you search for that new comment but you can't find it.
In regard to the order one thing I have seen is as I post it goes to the top of the replies, but if I refresh the page then it will be at the bottom.
I've seen it go to the top, but I didn't realize then it moved. But then, with those direct replies, it's hard to tell what order they go in unless you always look at the time they posted. The other thing about the direct replies is that after the third reply, or level, you are unable to reply any longer, so you need to start a new comment and reference the direct reply thread.
@Quicken Janean thanks for your reply
I understand completely. Personally, I would rather not use direct replies. They cause the comments to get out of chronological order and make the thread harder to read. The direct replies tend to collapse and are easy to miss. Sometimes the collapsed comments are an important piece of the conversation. I use the direct replies only when I think it's important to directly respond to the commenter..