With ESXi 5.5 Update 3, VMWare addes USB 3.0 Passthrough support. It does this via xHCI USB adapter and the necessary drivers.

When I upgraded from ESXi 5.5 Update 2 to Update 3b, USB 3.0 did not work, though. The necessary driver had not been installed automatically with the upgrade. So here is what I had to do (in PuTTY):

1. Install the xHCI driver from the bundle I used to do the upgrade:
   esxcli software vib install -n xhci-xhci -d "/vmfs/volumes/datastore1/Install/VMware-ESXi-5.5.0-Update3-3568722-HPE-550.9.5.0.33-Apr2016-depot.zip"
2. Restart the ESX host.
3. Make sure the driver is loaded:
   esxcli system module load -m xhci
4. You should now see your USB 3.0 device with:
   lspci
   lsusb
5. You can now add the xHCI USB controller in the VM and then add the USB device.