The biggest change is that it uses XPath for the dirty work, which makes it quite a bit more readable. It's 100 lines longer than the previous version, but it does twice as much.
Now both a [reply] and a [quote] link are added to each comment. Replying to parent comments now adds @username: to the comment field as well as the links added by the script.
Regression: The link to the parent comment is no longer displayed. If you miss this then let me know and I will add it back in.
Any comments, criticism or feature requests are welcome just leave me a comment here or on userscripts.org.