Sorry, yes, you're right - the latency overhead is not negligible (as a percentage, though in absolute terms it seems pretty tolerable).
Is this added latency just VXLAN overhead, or is flannel userspace still involved in per-packet-processing? I'd love to see a test comparing flannel/VXLAN to a manually configured VXLAN tunnel.
(I'm off to read the flannel code...)
To be clear, there is nothing fundamental (to the best of my knowledge) that would prevent Weave implementing a VXLAN backend. It is simply a poor implementation at the moment, and even then, only in this regard. Who knows, maybe Weave's use of a gossip protocol vs flannel's CP etcd could make it more suited to some deployments. Though, that does need to be tested.