This one is less nefarious, IMHO. Sure, a central server makes it easier to snoop. But, it also meant you could reliably get messages sent while you were offline. Skype had been built around desktops with consistent connections, but needed to adapt to intermittent connectivity of laptops and barely any connectivity of iPhone. Older smart phones like s60, blackberry, and windows mobile could support always on background apps, but iPhone only has very limited background execution, and it was originally much more limited... now you can do a voip push and do some communications before you post a notification, but around the the time of the change, notifications had to be composed on a server and sent fully formed --- there was no way to run code on push.
And supernodes had already been centralized.