Just a quick thought dump:
It has been seen over and over again, that people don't want and don't care about decentralized systems. Major problem is that decentralized systems are basically mobile hostile. Some companies have used these solutions to limit burden on their servers, pushing to burden to clients, which are then unhappy about it. Clients can consume a lot of cpu time, memory, disk space, disk access, cause lot of network traffic, be potentially used to generate DDoS attacks, or malicious traffic etc. All are great reasons why not to use decentralized solutions. Zero Configuration is also basically impossible because you have to bootstrap the network some how. Fully decentralised solutions still require bootstrap information. Which is unfortunately hats enough for many and therefore works add efficient show stopper. Last nail to the coffin is that most people really do not care about security at all. User base is after all just a small bunch of delusional geeks. Otherwise something like RetroShare would be widely used. I've been considering and wondering these same questions for several years. About bitcoin style messaging check out bitmessage. Yet it's also technically a bad solution, because it doesn't scale and client and messaging requires way too much resources. Especially when considering mobile clients.
More stuff about distributed solutions: I was personally quite sure that trackers and other download sites would be replaced with distributed systems. Instead sites like TPB and others continue to use centralized systems. I'm of course pro distributed & anonymous systems, that's the reason why I've been studying those for years. I'm kind of disappointed how little those are used, if used at all.
When TPB guys said they would make something cool, I naturally assumed they would release a fully decentralized, pseudonymous, anonymizing solution, which would replace Bittorrent which is inherently dangerous because it leaks so much metadata as well as reveals to whole world what you're downloading. Instead they released something (technically) lame, the piratebrowser. Which just allows accessing their site via Tor (basically working as proxy), even if it's blocked locally.
I really do like Freenet & GNUnet design, because relays do store and cache data, creating a lot of sources quickly for popular data. Many systems have serious flaws, bitmessage is not scalable with it's current design. Most of other fully decentralized systems suffer from flooding sybil and metadata leaks. I personally played a little with a bitmessage creating over 100k fake peers just for fun and it worked beautifully flooding the network with noise and generated junk control traffic. Because it's distributed solution, up to 10k junk messages were stored on each peer, wasting also disk space. Decentralized design also makes nodes running the system vulnerable unless additional steps are taken to limit resource consumption. After resources need to be limited, then it's a great question what should be limited and how that affects the network.
Like the original article says, it's really hard to come up with solution which wouldn't be bad in some way.
When mobile devices get more and more common, the fact is that it's really hard to beat the centralized solution. Of course the system can be partially distributed so mobile clients can connect to one spot only. Server hubs doing routing and data storage. But basically that's no different to email, DNS and web at all. So no news here either. After all, email isn't bad solution at all. It's secure (if configured correctly) and it's distributed. - Yes, I'm one of those running own email servers, as well are my friends too.
Final question is, how to protect metadata and hide communication patterns. As I mentioned in my post about Bleep. It didn't impress me at all. http://www.sami-lehtinen.net/blog/bittorrent-bleep-my-analysis
I'm not attacking the original article writer. He clearly has done a lot of job and considered options as well as written clearly and well about it. But I'm just thinking these issues in completely technical manners.
I'm happy to hear comments. I'm just cynical because the distributed systems didn't turn out as popular as I would have expected and wanted.
What I would like to see? A perfect fully decentralized P2P network running as HTML5 App which wouldn't require installation. That would be something which I would rate as pretty cool currently.