I'd like to see some new built in options for the comment management system in wordpress.
Two I can think off right off the bat would be the ability to a - write a return comment and b - write an email response. Both without leaving your admin/comment management panel.
I know there are multiple plugins out there to handle some of the aspects of what I'm thinking about but I honestly believe it would be best to be an actual part of the wordpress system. Especially considering the fact that you need one or two other comment plugins to make other plugins work for everyone.
Another useful comment addition would be to send an automatic email to commenters when the author has responded to their comment.