When I've logged into a shell as root (after logging normally as my user), I can't change the preferences of GUI applications when that preferences menu is only available in the MenuBar. 

For example, I like to change the theme of Gedit to a very obvious theme, so I don't forget I'm editing a file as root.

Here are my steps (Fedora 20):

1) Open Terminal and log into root via "su -"
2) Run "gedit"
3) Click on the application in the MenuBar

Nothing appears, since it's running as root. It's nice and tidy to tuck everything up into the MenuBar, except when trying to work as root.

As a work around until this is addressed, I can edit config/preferences files by hand. But it seems quite silly to have to do this; it's one aspect of Gnome2 I miss, and could trip up users more and more as Gnome 3 gets deployed to a wider audience.