Matthew, I appreciate that you're genuinely trying to make things better, and that you're being communicative here.

However, the statement, "we concluded that the notification area was a bad way to notify people," pretty much sums up the problem here: It might seem like a bad way for you, but it is definitely not a bad way for everyone. The change took many of us from something that was working quite well to something that works quite badly in comparison. In other words, it essentially broke things for existing users, which in software development is generally a sign of a bad change.

I'm not the least bit surprised to learn that this change was made in reaction to usability tests and focus groups, since those are notorious for failing to represent real-world usage. Obviously, this is an example of such a failure, since we already have a dozen people on the "affects me" list of this bug report, and those are just the ones who have enough technical knowledge and motivation to realize what happened, figure out the name of the debian package responsible for the notifications, search for it on launchpad.net, find this bug report, create or log in to an account here, and register the fact that they are affected. Considering the hurdles involved, I think it's safe to say that each person on the "affects me" list represents quite a few others who are unhappy with this change (or will be once they get around to upgrading from Raring or Precise).

My comment about Unity was not meant to suggest that the problem is caused by Unity. I only mean that this is not the first time since Unity was introduced that seemingly Unity-centric changes have been made that negatively impact non-Unity users. (The previous example that comes to mind is liferea having been modified to get rid of its notification tray icon, which is fine on Unity, but leaves the application completely inaccessible on other desktops!) In this case, there are at least two specific problems with the "new" update-notifier behavior on non-Unity systems:

1. When "unimportant" updates become available, update-notifier's only way of notifying the user is now to show a box on the Unity launcher. If the user is not using Unity, this might appear as a small and extremely easy to miss button on a narrow bar at the bottom of the screen (if the user happens to have a desktop panel that shows running tasks), or nothing at all (if the user doesn't happen to have/want a task bar on his desktop). This makes update-notifier effectively useless on such desktops, because it is not only failing to put a notification in the place where we look for notifications, it is actually not notifying the user in any useful way at all.

2. When "important" updates become available, update-notifier pops up a dialog box, immediately interrupting the user from whatever he was doing, which is very irritating. (I'm trying to remember whether it also steals keystrokes from other applications in which the user might be typing, as pop-up dialogs usually do, but I don't know how to trigger this behavior right now.)

As for bugs that you say were "directly caused by the existence of code to generate indicators and notification bubbles", I would suggest that the proper solution for such things is to fix the bugs, not to rip out critical parts of the software upon which users depend. If fixing them is difficult due to code complexity, perhaps a good compromise would be to simplify the code without eliminating the important bits. For example, I could get along just fine without notification bubbles, so long as an icon still appeared in my notification tray and allowed me to click it to see what updates are available.