So D2 now remembers what you have read. This will mostly be useful to readers who use the key bindings to navigate -- we didn't really want to guess if you've read something, but if you use the WASD keys to navigate, moving on from a comment flags it as read. Read comments are slightly faded, and if you re-enter a discussion a few hours later, it should remember what you've read.
We've simplified comment retrieval as well. If you get to the 'End' of a discussion and try to get more comments (either by clicking one of the various 'More' links, or by pressing a keybinding like S or D that tells us to move on to the next comment) a dialog box will show up asking you if you would like to lower your threshold. So if you normally read at Score:4, and read to the end of the Score:4 comments, it will offer to lower your threshold to Score:3 either for all time, or just for this page. This means you don't need to constantly raise and lower your threshold to handle discussions of different sizes. This works really nicely.
Lastly is a user preference in the pref pane labeled 'Collapse Comments After Reading.' I'm actually considering making this one on by default but I'm open to feedback. It does what it says -- after you've navigated off a comment (using the keybindings again), it collapses the comment you just left. This makes it very easy to keep your place in a discussion as it grows. This is especially useful in discussions where you want to leave a tab open for several hours, or else come back later and figure out what's new.
There are undoubtedly bugs: feel free to email me or post them to the bug tracker. Thanks to pudge for hacking all this stuff too. Especially the bugs -- he wrote those first.