I've refrained from the conversation thus far, because I wanted to read
through all of the comments first.  But as someone interested in HCI,
this is an issue of particular interest to me, and I feel like I need to
add my opinion.

Applications should *never* open without explicit action by the user.
This smacks of malware popups in Windows, and makes users feel less like
they are the one in control of their own system.  It doesn't matter
whether Update Manager opens above or below windows, because it
shouldn't be opening automatically in the first place.  In addition to
fostering the users' mistrust, it would almost certainly only result in
click-through behavior as users try to get rid of the offending
spontaneously-opened window.

The notification area is not, IMO, broken, as has been stated by others.
It is certainly *misused*, and I agree with the idea of moving things
out of the notification area that don't belong there.  There is little
reason, for example, for a program to have a constant icon in the
notification area, or to minimize to the notification area.  (Of course,
these things can only be fixed by the software developers, so there's
not much we can do about it.)  But when used *correctly*, the
notification area is perfect for what it is designed for -- non-
intrusive persistent notifications.  Notify OSD is great for transient
notifications, but lousy for persistent notifications.  And update
notifications definitely fall into the persistent category.

So here's my suggestion.  Go back to the old behavior, with a slight
modification.  The old notification icon should appear in the
notification area when any updates are available, and remain until the
updates are installed or selected to be ignored just as it did before.
But in addition to the familiar notification icon, a Notify OSD
notification should alert the user when important updates are released,
and continue to appear at login and perhaps periodically (e.g. once an
hour, or every 6 hours) until the important updates are installed.  But
the Update Manager should most definitely *not* be opened without direct
user action.

-- 
[Jaunty] Update Notifier icon would provide useful status information
https://bugs.launchpad.net/bugs/332945
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