I agree with most, if not all, of the proposed changes to the notification system. I agree, for example, that notifications are just "extra information" if you happen to be present and shouldn't require interaction. However, that's not to say that I don't think it would be convenient to have a gesture/keystroke shortcut that causes a predetermined interaction with a notification type. For instance, it would be convenient for me if there was a short snippet about each incoming email, displayed in a notification, as opposed to "1 new message". That way I could know if the email was worth checking or not. If it was, it'd be nice, at the time of notification, to hit a key combo or something that took me straight to mail to see the new content. While I think that's a great idea, I have no idea on how to implement it in such a way that doesn't negatively affect other users.
I think one of the longest standing problems with Linux is the tray / notification area. Too many competing methods, sloppy looking icons, and inconsistencies that create a negative experience for the user.