Another problem: I've never seen a meshnet protocol that isn't vulnerable to a variety of flooding, cache pollution, DDOS, and other attacks that could basically make the network unusable.

This is a problem for the idea that mesh nets should be used to create resilient decentralized networks. Unless the meshnet is safe against attacks, any government or other organization that wanted to take a meshnet down might actually find it easier than taking down a multi-path tree-shaped or centralized infrastructure.