The Skype-Killing Box → The almighty $$$$$

VoIP companies are scared of losing business, so they put pressure on ISPs(who also want a share of the VoIP market).
Then combine this with the fact that ISPs are looking for ways to limit their broadband traffic so they can have more customers on the same lines without spending money to increase lines and bandwidth.

One solution would be to encrypt all information in a way that packet analyzers can't determine the content being sent/received. This will most definately come at a cost to performance, but in the end you will have anonymous packets which can't be filtered because there is no way to tell if someone is streaming video or music, playing video games, making phone calls, downloading programs/files, etc.

There is no way to stop people from using a service which they pay for unless they shut it off.