I do think that darknets (like I2P) start with encryption and build on that. You can choose the number of additional hops used for each application down to 0 and the link stays encrypted.
It seems that its the attack you describe which is very difficult; the attacker would have to masquerade themselves internationally on a huge scale. The NSA doesn't seem able to manage this with Tor, and I2P makes the problem more difficult where everyone is re-routing others' packets by default. So just collecting the metadata becomes orders of magnitude more difficult.
For that reason (making mass surveillance prohibitively expensive) Bruce Schneier has called for better-integrated anonymity tools and sees a larger role for them. The additional benefits are well worth it: A cryptographically-based network address that no ISP can censor, and which becomes the basis for a type of identity that puts disclosure entirely under the users' control.
I say integrate I2P to the point where they are assumed to be the normal network stack-- under normal circumstances don't even use apps that use plain TCP/IP; Cover everything with encryption by default and have every app show the level of anonymity that the user can adjust like the volume slider for audio.