The thing that immediately stands out is the routing. It looks like cjdns is a traditional-ish multi-hop network. The DHT routing table allows you to map out a route to peer A via peer B, R, & D.
What wireguard and nebula allow is for the underlying network to figure out most of the routing, and effectively create a massive point to-point network. whilst you can have concentrators/gateways, the idea is that most of the traffic goes direct from peer to peer. This can reduce load considerably.
I think cjdns allows arbitrary peering, so you can certainly set up a full mesh if you want point-to-point traffic, with multiple hops only for cases where the underlying network topology requires it.
