Good question. The obvious errors were 1) artificial scarcity - too small address space leading to a situation where direct connection/communication between members is impeded by various NAT schemes; and 2) too naive attack-susceptible protocols allowing subversion of DNS, IP routing, email forging/spam. If we ever start again, the system should solve at least these issues.
The bigger issue is the control over internet services that we are witnessing (deplatforming, censorship). Technological ideas can help to prevent those but I tend to think no matter the protocols chosen, it will be the powerful who have the most power to control the network. So better design it in a way that no single power can control it all.