Technically there are some cases where it would make a difference. Generally speaking even when this difference exists, it won't be noticeable to even a professional player.
USB 3.0 and USB 2.0 controllers on modern motherboards are implemented differently, primarily due to the data throughput USB 3.0 requires. In some chipsets you'd find the USB 2.0 appear as essentially PCI device on a supercommunications hub that also handles all the other slow devices, like hard drives, audio, ethernet, parallel and serial ports, etc. This existed in the southbridge chip, which was then connected to the northbridge through a media layer similar to a PCIexpress bus. The northbridge handled the high speed stuff, such as memory, graphics, PCIexpress etc.
This meant that a USB transaction involved several other transactions - PCI, then the media interface, then the interface to the CPU, before it was handled.
USB 3.0 was introduced at the same time that the northbridge/southbridge gave way to the PCH(Platform Controller Hub). Most of the northbridge duties were absorbed into the CPU itself - memory, PCIexpress, etc, while the remaining northbridge duties and southbridge duties went to the PCH. The PCH is essentially running off a PCI express slot.
The paths, however, are still very different. Even though USB 3.0 and USB 2.0 are integrated into the PCH, the USB 2.0 is still implemented as though it's a slow PCI controller device. There's no reason for Intel to redesign the silicon of a proven part, so it's integrated into the PCH the same way it was integrated into the southbridge, with all the attendant bottlenecks and additional latency that it had before.
However, the USB 3.0 is much closer to the CPU. While this is meant primarily to account for the increased throughput, it also affects latency - there are fewer transactions involved in getting a USB 3.0 transaction to memory, or to the CPU, and the interrupts may be triggered more quickly.
However the difference between USB 2.0 latency and USB 3.0 latency would be measured in nanoseconds. Certainly not noticeable by even the best twitch gamers today. It exists, but it's practically useless.