How many of these P2P overlay networks could run without a centralized head/mapping server? BitTorrent has drastically reduced the size of theirs, but it still needs a mapping of other hosts somewhere. Same thing for Skype. I don't want to sign up for an internet where every connection needs a 'head' in order to determine how to traverse the overlay network.

It's probably also not a coincidence that Skype and Bittorrent are two of the hardest protocols to 'control' inside the network. This sounds good from a 'the internet should be a free democracy' standpoint but bad from a 'let's guarantee the performance of the application' standpoint. In terms of visibility into what is happening, being transferred, and where connections terminate there are more productive rather than draconian reasons for understanding those things.

Today with virtual hosting if the website next to you decides to host illegal content, the entire IP is taken down collateral damages or not. Well, that's part of your choice in choosing a provider as an end host. If the entire next generation internet and application space is based on overlays and other nebulous architectures, much of those same problems are going to exist to larger scales, including at transit points. Except it won't be as optional as changing hosting providers.

Since you've got BGP experience - think about the fun in troubleshooting eBGP neighbor problems when every connection is a GRE tunnel that may actually be tunneling through another BGP AS, which itself may be tunneled again. GRE tunnels are great immediate bandaids and generally awful long term solutions for enterprise networks to say the least. But the application guy gets his green light and thinks everything is great.