I think most of the issues I've had have been resolved by the use of themes, but I still have a couple issues.
When loading a message that has several group members, about half the page at the top is full of the member list and their icons. I would prefer not seeing that.
Also, in the notification window, when you click a comment it takes you to the beginning of the thread instead of the comment you are clicking on. I would imagine that would be able to be fixed similar to the behavior of the forums.
Thanks for the hard work put into the site -- the transition hasn't been too bad :-)