Good point -- there are notifications the user wants to see at a glance, without having to click an icon and navigate its sub-menus.
One way this could be handled is to add another option that appears when you right-click on a notification: "add icon to systray". That would bring up a configuration window with:
- name of app/driver sending the notification
- icon to be added to systray, with button to select a different one
- radio buttons:
x pop up message windows above systray icon
x click systray icon to see messages
Right-clicking on the new app/driver-specific systray notification icon would give you an option "move to universal notification icon" that would undo the steps above.
Probably most distros would ship with a standard configuration that would have separate icons for things like battery and wireless. And if the user didn't like those they could easily get them out of their systray and into the universal notification icon.