This may be hopelessly naive, as I've not followed any of the Ubuntu discussion except for the succinct summary in this article. BUT, how about having a single notification icon in the system tray. It would normally be grey, very easy to ignore. If an application had reason to notify the user, it would tell the daemon behind the systray icon. At the point the systray icon would turn red (or some user-configurable color / shape) to indicate that there is at least one notification awaiting user input. The user can choose to ignore it or not, depending on how they are using the system at the moment. If the user clicks on (or hovers above? -- perhaps again user-configurable) the notification icon, they get a menu listing the applications that are currently attempting to notify them. They select which app (maybe including "all") and all of that app's notifications are displayed. The user responds to each in turn, and they disappear from the universal notification icon menu. When there are none left, the systray icon turns back gray.
This seems to me to have the following benefits:
1) All notifications appear in the same place, no need to go hunting for them.
2) Notifications are easy to ignore (or not) depending on how you're using the system at the moment.
Maybe this completely misses the mark, I don't know. It just occurred to me as I was reading this article.