Threaded comments have advantages but they also have disadvantages. I won’t mention the disadvantages because if you don’t know what they are already than they aren’t disadvantages to you. The advantages are: 1) You can keep track of a sub-conversation in a comments stream; 2) You can refer to a specific upstream comment easily (which in non-threaded contexts often uses a reference to a comment number, which has the disadvanage of not being fixed if old moderated comments are inserted prior to the numbered comment); and 3) at least in some cases, you can subscribe to a specific comment (like on you just made) to see only responses to it and not to the entire comment stream.
It seems to me that we can have our cake and eat it too.
What is needed is a convention by which a comment can be linked to a prior comment. So, when you are making the comment. This can be done in several ways, including:
1) You hit “reply to comment” on the comment to which you are replying, and you make your comment. However, visually, your comment will not be threaded under that comment … it will just go at the end of the comment stream as the most recent comment. However, it will have a header that indicates what comment it refers to and you can click that to go right back to it.
2) You simply use a particular bit of text using as standard format referring to the number of a numbered comment. Like  for comment 123. Later, if the comments are renumbered that reference gets changed appropriately (or changed to a [comment removed] if it is removed. This code also supplies the data for the linked comment navigation referred to already in 1) above.
3) Some kind of menu that lets you access a list of prior comments.
This would prompt a comment navigation system which would have the following features:
1) User can fold the comments into threaded form or unfold them into sequential form;
2) User can find a link to the next sub comment at the bottom of any comment to which a referal was made, and follow through all the threads this way, using a simple visual navigation system;
3) Since this will get confusing no matter what, the user can mark a comment “read” and thus, later on, look at the comments that are not read in any of the available layouts; and
4) The user can see a visual tree of all comments with the usual annoying ballons popping up out of nodes on the tree.
OK, WordPress coders, let’s see what you can do!