Is there a reason all the current USB 3.0 motherboards also have USB 2.0? With 3.0 being adopted by all the big players and being backwards compatible to 2.0, I don't see a reason for the 2.0 ports to persist. I would almost certainly give preference to a board 6 or more 3.0 ports over 2-4 3.0 & 4 or more 2.0 ports, all else being equal.
As mula said, they are 3rd party controllers. The big fault with this is they do not initialize until you are in windows which means no booting from usb, no keyboard or mouse in bios (which you can't even get to) or during the windows installation. I don't agree with anything else said.
IB will have native usb 3 but still has 2.0 ports. This is probably due to some bandwidth limitation.