I had some issues with usb 3.0 to up my polling rate to 500 with my wmo in win7... had to disable it to work as 2.0.

aside from that I doubt there is any difference.

there should be no difference, as most HIDs are actually using 12Mbps full-speed USB 2.0 spec

use the usb ports of the intel controller.

Doesn't matter as all ports have the ability to route to the compatible host controller chip. Back panel ports should be preferred over front panel.
You could disable your 3.0 chip if you don't really use bandwidth-heavy devices (i. e. if you don't use swap media to transfer stuff that often). Just to be sure the 3.0 driver/chip doesn't interfere somehow.
Or go more extreme and disconnect your front panel ports and disable all host controller and deinstall hubs you don't use.