I've been very optimistic about the capabilities of darknets/meshnets, especially cjdns, since it is simple to implement and still a very well thought out way of routing and building a network. But I think the major flaw of darknets and meshnets is that the usefulness of a network depends partially on the number of users. The more users, the more connectivity, speed and activity. It's the reason why people use facebook, and not a competing social network: because everyone is on facebook. There has not been a darknet/meshnet that has been widely adopted, thus the usefulness of the information that can be found on such a network is limited. It's kind of a self fullfilling prophecy, and until the majority of people start to care about a mode of networking that is more secure I think that these kinds of things will remain a thing of hobbyism/nerdy passtime. Same thing with encrypted email, file encryption, etc.