USB 3.0 isn’t necessary for controllers, there is no real need for the extra bandwidth. I’d personally hook up my controller directly to USB 2.0 port, the external HD to the USB 3.0 port for optimal performance. Leaving you with one USB port free. If you plug in your wireless mouse, you’d have no more USB ports free, but no need for a hub right?
If you do want/need more ports, like Todd said get a powered USB-hub, hook it up to the 3rd USB port (the 2.0) and put wireless mouse and whatever else you need that is less mission-critical than your controller and HD on the hub.