One possible solution is to use flat view, like in the Comments stream, but localized to an article, with the links to a threaded view, linked to from the list of articles. Also, this list of articles should probably show title only, without summary parts of the text.
[Edit: Issues, Bugs, and Requested Features should be tracked at Google Code, not here -- matt, 2010-04-23]
Less Wrong is still under construction. Please post any bugs or issues with Less Wrong to this thread. Try to keep each comment thread a clean discussion of each bug or issue.
Requested features... sure, go ahead, but bear in mind we may not be able to implement for a while.