I can't agree more with the sentiment of those that want the old functionality back. Security update or no, I don't want to wait a week to be notified and then be either notified by an abrupt "in your face" pop over or a "you'll never see me" pop under.
Since starting to test Jaunty I've repeated encountered application crashes (npviewer.bin, as I recall) that apport won't let me report as the system is lagging behind on updates I wasn't aware were available since I was expecting the old behavior.
In short, security update or not, I would like to be notified in a obvious and unobtrusive manner that there are updates available as soon as my system knows that they are there. I would like said notification to be persistent but unobtrusive. I felt the method used in Intrepid and prior worked fine. I don't care for what I've seen of this new method at all.