[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.
Yes, and this seems to be a general issue of how comments are represented in the discussion (tree view) vs. how comments are tracked by various means (individually, without any context). The difference in presentations leads to difficulty in understanding the same comment when it's written and presented in different modes.
For example, if the discussion itself proceeds in linear view, people refer to comments to which they reply, or cite them, which makes reading comments linearly simpler. It'll be simpler to read such comments in e.g. a feed reader. On the other hand, when the discussion happens in tree view, comments are written without mentioning their context, and as a results comments streamed into a feed reader individually become incomprehensible.
We need some kind of linear view that cites its context. I suggest (an option for) including comment's parent in all kinds of local or linear views for comments, including feeds.
Specifically for the problem pointed out by Michael, maybe there should be some kind of "subscription" capability, through which you form a set of comments, replies to which get aggregated into a separate feed (or discussion-like stream, like any of the many views that present the content of the site).