Not that anybody in a position to do anything about it is likely to be listening, but it would be really cool if I could reply to comment notification emails and have LJ do the right thing.
That is, when I get an email from LJ that someone has replied to my <post|comment>, I want to be able to reply using my email client and have my reply appear in the appropriate comment thread, threaded correctly. It wouldn't be hard, and it would be really helpful not to have to open a web page just so I can read what I've already read and then enter my reply into a textarea (or use "It's All Text...") instead of using the editor my mail client is already configured to use.
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The problem is that having implemented something reasonable for HTML email, they think they're done.
The problem with -that- is that even ignoring text-only browsers, it is entirely an inadequate solution for mobile devices.