Maybe I am too late and maybe most things already been posted but still I am adding some points if something missed what I am thinking.
Better User Profile Page:
Where any user can find almost all statics of the user. How many question been asked or answered, comment, points, vote etc. like stack overflow.
Direct link in notification email:
Now email notification contains only question link. That would be great if it provide direct link of the answer or comment so if there are many answers or comments than no need to find new one rather link will directly take there.
I just wonder and don't know what I was looking in my email but seems I found that email links are pretty okay :P extreemly sorry for this.
As some of the boards are very busy and that is always good if content loads without refresh after certain time of interval via AJAX.
I think this point has already been mentioned that live notification on the login bar.
Required Plug-in Sub Pages:
It is becoming too much to manage on the same page if board has more than 5-10 plug-in installed. So can be great if plug-in page will have own vertical navigation for each plug-in and loads plug-in setting in the right side of content area. This can make admin’s life easiear than now to jump and scroll up and down. So layout for the plug-in page will become three columns. In fact removing widget (sidebar) area from admin section is also alternative as it is not so useful. Anytime if admin want to see the updates on the sidebar he can go to the front end and check or can open another window than just refresh the update.
Include Plugin from the contributors:
I think now you should include few very useful plug-in by the great contributors. Some of them like Badges from NoahY, Widget Anywhere from Scott, Accept Rage by NoahY also User per Month by Kai etc.
HTML structure flexibility:
This may be huge work to make it happen and don’t know is it possible or not in reality but my idea behind this is to create some more flexible system like WordPress where user can define them own HTML structure while design the theme.