Sorry for not replying sooner. Some of my recent time was, unfortunately, spent undoing the work for getting people to use group messages instead of secure categories (what we, rather confusingly, call “closed groups” in my system). I’m now in the process of moving everyone back to secure categories and using my “watch categories” plugin to enable notifications 
Broadly, I agree with Tobias. I support the idea of having just one inbox with everything in it.
I would like to maintain group inboxes, but I would prefer if they functioned as filters/labels rather than as buckets. So, if a message is sent to @foo-group, it should be available both in my personal inbox and (if enabled) my “Foo group” filter.
I use the inbox as a dashboard to see what’s on my plate, so I need to all “active” messages there. It would be a PITA to have to click through multiple groups to view all active messages.
Here’s how I envision the sidebar:
- Inbox
- Archive
- Group A
- Group B
- Group C
etc.
Notice that there’s only one inbox and one archive, which work as you might expect. The inbox contains all messages that have not been archived. The archive contains everything else.
The various groups would list messages sent to that group regardless of whether they are archived or not. When you are viewing the messages in, say, Group B, there would be a section for messages in the Inbox and a section for messages in the Archive – but all on one page.
Average users can just work out of their inbox. Users who need to get an overview of group activity can do so using the labels.
I think this would work for most cases without requiring additional configuration.
Tobias, in such a case, would you still feel that it’s worth turning the group labels on the side on/off?