Why won't USB 3.0 external hard drive run at USB 3.0 speeds?
Solution 1:
Are you sure the disk is plugged into the correct (USB 3.0) port? It looks like your USB 3.0 controller is providing USB bus #12, but the disk is attached to USB bus #3.
According to your dmesg, USB Bus #3 is provided by the PCI device '06:01.2: USB Controller: VIA Technologies, Inc. USB 2.0 (rev 65)', which will only be USB 2.0.