A single x1 PCI-E 2.0 lane oscillates at 5 GHz, and
each byte has one extra start bit and one extra stop bit,
in addition to 8 data bits, OR 10 bits per byte.
Thus, 5 GHz / 10 = 500 Megabytes per second
in each direction (max bandwidth) per PCIe 2.0 lane.
USB 3.0 is 10 TIMES the speed of USB 2.0,
or 10 x 480 Megabits per second = 4.8 Gb/sec.http://www.everythingusb.com/superspeed-usb.html
Again, each transmitted byte has a start and stop bit + 8 data bits.
Thus, 4.8 Gbps / 10 = 480 Megabytes per second.
So, the limiting factor is the USB 3.0 bandwidth (480)
not the PCI-E 2.0 bandwidth (500).
Of course, controller efficiency is a factor too,
but no controller can exceed the rated max bandwidth.
Hope this helps.