I'm not even sure if you CAN change any of these things:

1) It's much more difficult to tell which posts are new, regardless of which scheme I'm using. Not sure if this is color-blindness related, but it seems that the "new posts" icon and the "no new posts" icons are really similar. The flaming versions are essentially identical, as far as I'm concerned.
2) When I click on the "last update" icon (three dots in a triangle), it only shows me THAT POST, it used to show the entire thread but starting at that location.
3) Threading only shows in the headers at the top, I've also seen where the body of the message is slightly indented. This is useful since it's difficult to remember where a particular thread goes in or out.

Take a look at my options, maybe some of this is related to something specific I've set without realizing it - in which case, please rethink the descriptions of the different options, where possible & relevant.

I really like how sub-folders are shown in smaller print next to the main folder, it makes it easier when you like going there frequently, such as the vendor folders.