If you use FT 6.0 (with more than one vCPU) and you experience high latency and low throughput, you should check your ESXi 6.0 patch level. This is a known problem which is addressed in the VMware
ESXi 6.0, Patch ESXi600-201608401-BG.
"When Fault Tolerance is enabled, the FT protocol might encounter a race condition that results in large increases in guest VM network latency and decrease in the VM network bandwidth."
And always keep in mind, that the new FT version is heavily relying on the FT link. So please use a dedicated 10 GBit network and take a look at this whitepaper.
VMware vSphere 6 Fault Tolerance Architecture and Performance
