Much of the reason for USB's slow disk performance is the simplistic bulk-only transport protocol used by virtually all USB mass storage class devices on the market today. The problem is bulk-only transport is a synchronous protocol, where every transaction must be fully completed before the next is begun. Even though it's transporting SCSI commands, you don't get important performance enhancing features, like command queuing. It's impossible to make best use of USB scheduling by sending the next command before the previous fully replies with the status code.
There is a new protocol called UASP (USB Attached SCSI Protocol) which aims to fix all this. But who knows when or if Microsoft will ever support it?