You’d think that identical host controllers would provide similar performance, regardless of how they're implemented (or at least that motherboard vendors should achieve similar results by intelligently adding this functionality). However, existing USB 3.0 solutions vary for two possible reasons. There may be differences on the driver side, and performance depends a lot on how the controller is attached to the host system.
Stand-alone cards may be bottlenecked on older PCI Express systems, as well as practically all Intel machines that implement PCI Express 2.0 only on the graphics interfaces. In case you aren't up to speed on the situation there, the company's Lynnfield- and Clarkdale-based desktop processor employ an integrated PCI Express 2.0 controller limited to 16 lanes. The remaining connectivity comes from chipsets like P55 and H57, which run at PCIe 1.1 signaling rates, thereby handicapping performance.
USB 3.0 cards inserted into PCIe 1.1 slots might face throughput limits. However, this isn't always the case. We measured our lowest throughput of 113 MB/s on a Gigabyte P55A-UD6 with an onboard NEC USB 3.0 controller and the fastest throughput on the Asus Crosshair IV Formula using add-on PCIe 2.0 cards from Gigabyte and Western Digital. Combined read and write operations were fastest on stand-alone controllers with sufficient bandwidth, and on the Gigabyte P55A-UD7, which switches PCI Express resources.
In the end, we can’t speak for or against PCI Express 2.0 add-on cards for USB 3.0. They all deliver sufficient performance for today’s devices, such as Super Talent's RAIDDrive. Yet, we strongly recommend operating these in true PCI Express 2.0 slots for maximum performance. If you want a motherboard with an integrated USB 3.0 controller, you should definitely consider product reviews that include USB 3.0 performance evaluation, given that seemingly-similar products, such as Gigabyte's P55A-UD6 and -UD7, deliver markedly different results.
We also found no reason to shy away from a USB 3.0 hard drive and controller bundle, such as WD’s MyBook 3.0. So far, all USB 3.0 products are based on the NEC controller, and none of them are bad.