I think the menus will be more customizable if it has a default css class and options to change it per-submenu. So, we can make the menu has variable colour, or variable font size or etc.
With the default css class, newbie user no need to input css class/css language.
And with custom submenus option, every submenus can be set to special one. if she/he understand it she/he can use this option.
Like the "Download" button on this site, and more than it, we can make more special button for "Free Download". Or for "Special link to a friend" or special link to "My favorite Sites/Forum". or etc ...
So, the WordPress Theme can be more customizable. And special! :D