I've given this tons of thought, and to be honest, haven't hit on a solution that I think would be a fix-it-all solution. Some thoughts though.

a) "Private" neighborhood mesh networks should be more heavily utilized. They would be "private" from the rest of the Internet, but "public" in as much as they are community based / owned.

b) We should admit that cryptography is here to stay, and work with that assumption. End-to-end encryption doesn't automatically provide 100% anonymity. The traffic movement can still be traced. This is much like a car that is being followed by law enforcement from one private residence to another. Law enforcement doesn't yet know what is going on in either residence or in the car, but can still do there job, and eventually law enforcement can target a weak-point in the activities that does not rely on encryption, such as talking to neighbors, turning suspects into cooperating witnesses, or investigating legal activities such as bank statements. My point is, encryption is here to stay, and if good citizens can't use it, whatever, "criminals" (and political dissidents and victims of domestic violence, etc.) will use it. Additionally, in my mind, encryption should fall under the protection provided by the second amendment. It's important to remember that the second amendment was meant to allow citizens to arm themselves to protect themselves against the government in times of war. It was not meant to allow for folksy looking guns to go hunting for Bambi.

It might sound like I'm going on a crazy tangent, but consider what a decentralized web requires. It requires it's constituent parts to be equally robust. If they are not equally robust then there will quickly be a "winner takes all" shuffling of the lines of communication. If your local network is not robust, you're not going to use it for banking, health care, government communication, etc.

So, a decentralized web will be a "confederacy" of networks, each of which can choose to be equally robust in terms of network speed, capacity, and security. It isn't necessary that each is equal, but each must be allowed to be so if so desired.

c) Between local or regional networks a federal network would provide much the same purpose as the federal highway system currently does for car traffic. I say this to mean the same purpose both as relates to 1) physical movement, 2) freedom to execute such physical movement, and 3) legally enforcing certain rights and restrictions as relates to such traffic. 1) The federated networks work provide physical infrastructure for the traffic and provide financial and administrative mechanisms to make such traffic a reality. 2) The federated network would politically / legally enforce the equal rights of individuals belonging to regional / confederate members to participate in taking advantage of the federal network. 3) The federated network would enforce laws and regulations on the "restrictions" sides of things as well, such as "no illicit" packages.

One difference between the real world highway system and what I'm describing here that is of interest is the potential for overlapping boundaries of the smaller (confederate) members. So, provided there is "region a", "region b", "region c", and the "federated network", "region b" might overlap some with "region a" and some with "region c", such that an individual in "region a" could send a package to "region c" either via the "federated network" or via "region b", provided the individual is fine with the terms set by "region b".

d) Provided you're working within the framework described above, I guess there will be P2P, IPFS, and other protocols. So, I suggesting that a major component that is missing is the communities, the goverment components. You can come up with all the protocols you want, but until they are required by the governments we legitimize, then they are not going to change society. So, in summary, it's not a technical solution we need, it's a political.