I just wanted to open up a thread about this.
It completely depends on your drives..
I've got a Pegasus R6 which runs at 680 mb/s - impossible via usb 3.
But today I got a new Crucial mx100 SSD in an external usb 3 enclosure. It runs at 430 mb/s on my macbook air, very nice.
But on the nMP it only gets up to 350 mb/s and gets capped there.
Is this due to the non-standard usb 3 implementation (dont know how else to call it, but I read that they somehow put a 3rd party chipset on the board since the cpu chipsets didn't support usb 3 yet).
This is quite a bummer, since I would've gone straight away for a thunderbolt enclosure... 🙁
I think other people on this forum have also reported not getting maximum speed from a USB3 device on the Mac Pro even if the device can deliver the speed on other computers.
They do use a third party chip by necessity, but that's not the problem. In fact, ironically, the manufacturer touts that chip as providing maximum USB3 speed on all four ports simultaneously (which not all USB3 controllers can do).
In order to get that speed, you need to provide enough PCI lines to the chip. Well, here's the layout according to the Anandtech review: the chip set has 40 PCIe 3 lines, but 32 of those are gobbled up by the graphics boards and the remaining 8 are routed to a multiplex chip to service the Thunderbolt controllers.
That leaves 8 PCIe2 lines that the chip set also provides. Four of those go to the internal SSD drive, and out of the other four, one goes to each of the two Ethernet ports, one goes to the wireless, and one goes to the USB3 controller.
So that's the problem, only one PCIe2 line to the USB ports. It's especially annoying because they blew three lines on the networking stuff when one line was probably sufficient for all three; and the second Ethernet port probably goes unused by most people to boot.
Well, for regular old single hard disks it's probably not an issue -- they don't come close to saturating a USB3 line anyway, and Thuderbolt would be overkill for those. However, if you are attaching anything high speed like an SSD or a RAID array, I personally would avoid using USB3 on this machine.