I only use WPMU for testing plugins, but I found the automatic activation of the admin bar to be one royal PITA. Surely it would have made more sense to have it disabled by default, and allow people to enable it if they wanted.
Additionally, I have one plugin active that created one top level menu item - that caused the admin bar to go onto 2 lines - badly - at my screen size. When I eventually found the setting to turn it off I was surprised to find so few settings. Surely there should be more you can configure to make it even remotely useful. Things like using the icons instead of text would solve a lot of wrapping issues.
I also think that replicating the while menu, unless you are going to remove the standard left hand menu, to be OTT - so another setting to choose what is displayed might make it more useful as well.
Apologies if thisis in the wrong section.