The rest of your post would be more useful with some specifics.
I translate this as: "I don't know how to make a solution. Please tell me how." Which is often followed by "It won't work."
As for VM's, it's true what you say. But at some point if you are connecting to a global network (internet), there is a physical machine that has to connect. And that machine needs an address which cannot be "faked up". Indeed, you some sort of authority to make sure people are not using the same addresses.
Nodes need a way to find each other. Routing tables are simple enough and they work. I will leave that alone.
But people have come up with all sorts of complicated schemes to try to allow nodes to find each other in a decentralized way, namely DHT type stuff and progeny of DHT type thinking.
But who says you have to mess with (replace) the existing infrastructure? Maybe you can just build on top of it. Maybe the exiting infrastructure is a bootstrap. The buzzword is overlay. Old hat, right? Well, almost nothing is truly new. And still, the overlay approaches people know about are often mindlessly complicated. We can do better. Some have done better.
NAT doesn't try to replace the existing framework. It just deals with it.
It isn't pretty, but this is how we are all connecting, in spite of all the IPv4 policy nonsense. NAT solved a problem. (And created a new one, arguably.) Whatever. It works.
There are easy ways for nodes, with crusty old IPv4 addresses, to get through their crusty old NATs and get open UDP ports to communicate with each other. They are not new. And they work. Gamers have been using stuff like this for decades. But there's a lot more utility to being directly connected than just playing games. Enter Skype.
Once that's done, once we're connected directly, we can forget about overblown global routing tables, brittle BGP, DHT and IPv6 dreaming. We can use plain ole Ethernet, we can keep our own small arp and IP routing tables, we can use private address space (or whatever numbers we want - it's our private network) and MAC's. We can run our own DNS. We can keep things simple and secure. Because we can have small private networks. We can manage them ourselves.
The global network was means to an end: finding each other and conecting directly. It was a bootstrap. If it runs on crusty ole IPv4 and depends on NAT and swollen routing tables, so be it. That's not my network. It is just a means to an end.
Personally I never understood the lure of connecting to a "swarm" via some DHT. And this is the thinking that has pervaded peer-to-peer. The concept of connecting to strangers, something like Chatroulette, is not really interesting from my perspective. But a lot of technically capable people think that sort of thing is worth their time.
I want to connect to my friends and family, not random strangers. I want to use the internet for all the things it's been cracked up to be for so long: a replacement for postal mail, telephone, video conferencing, etc. And I do not think I am alone in this view.
It's not a new idea what I'm getting at: breaking things into smaller pieces to manage them. What is the internet after all but a conglomeration of ASN's -- smaller networks.
"BOOTP for the global internet." A way to find each other. And then a way to connect. Opensupernodes. The rest, what you do after connecting, is up to you. That's _your_ network, not Facebook's, Google's, Microsoft/Skype's or anyone else's.
Cooperation, interoperability, (at least ostensible) simplicity. People's comfort with working and playing in small groups. These are the important points in my mind.