It's really late, so I hope I'm explaining this reasonably ok...
This is just an attempt to provide a few reasons why some people may conclude they see a difference in mouse operation "due to" USB2.x vs. USB3.x.
There are some conditions under which one might see what LOOKS like a 2 vs. 3 difference (stuttering, tracking delays, etc) on a USB2.x port and not see them on a USB3.x port on the same system.
An instance may occur if one is sharing the bandwidth of a given USB2.x controller with other much higher bandwidth devices. The thing is, one may not even know one is doing so! For example, if one is, in addition to the mouse, running other devices that are real bandwidth hogs on the same controller (note that "separate" external ports may use the same internal controller), or one is using multiple external hubs and multiple devices on each hub on a single external port, etc. However, if one moves the mouse and those same devices with the same topology to a USB3.x port on the same system, since the USB3.x subsystem has a higher bandwidth, any mouse degradation symptoms seen before may disappear.
One can use the Device Manager (or equiv utility) to examine the details of "Universal Serial Device Controllers" distribution. One may also get an idea of how the motherboard groups the USB ports/controllers if the motherboard user manual has a "Block Diagram". You might find a way to optimize spreading the bandwidth hogs over multiple separate USB2.x controllers to eliminate or reduce observed "mouse issues", if any.
One might also see differences that may SEEM to be due to USB2.x vs. USB3.x but aren't really intrinsic to the differences in the USB standards or bandwidths. Rather the differences are with the hardware architecture (e.g. chipsets) and firmware of a specific USB subsystem implementation, how a system handles interrupts under various load conditions, and so on. Where one motherboard may show degradation with a given device topology on a USB2.x port, a different motherboard may not even though they the devices and software are otherwise identically configured and both using a USB2.x port. So what looked like a USB2.x vs USB3.x difference on one motherboard was actually due to other factors. In other words, USB2.x (that had mouse issues) on System A may be implemented at the lower hardware and code levels quite differently than the USB2.x (without mouse issues) on a different System B.