Stop this. The sky is not falling.
Skype itself, today, runs over the general Internet, and got to its current position competing against an entrenched dedicated network that literally had been optimized for decades. (Aka the telephone network.) Oh, and one that is prioritized over general internet traffic.
In the nightmare world that you describe, any new Skype competitor starts with access to a better Internet than Skype did. Their main worry should be that Skype itself already exists, but for some strange reason Skype is choosing to spend hundreds of millions to billions making Verizon happy. And at the same time our new upstart can deliver to the exact same customers at very little cost! (Certainly a lot less per customer than Skype is paying.) Were I that entrepreneur I'd be crying, "Woe is me, don't throw me into that brier patch!"
And by this agreement, Verizon et al can't shut off this upstart service because guaranteed customer access comes straight from the consumer protections they've all agreed to.
In effect it is, "We have net neutrality, but the ISPs and anyone they can convince are allowed to waste as much money as they want in producing services with premium access." Given the history of the Internet I have no doubt that much money will be so spent, most of it will be wasted, and innovation on the Internet will prove to have been well protected.