I don't understand why new motherboards contain USB 2.0 ports along with USB 3.0 ports. There is no need for them. it only takes away from the USB 3.o that could take it's place.
For now it is a matter of economics. It is because existing chipsets already had USB 2.0 ports. When USB 3.0 came out they added additional chips to add it to the motherboard. I am sure at some point there will be new chipsets that have native USB 3.0 ports.
An example is the GA-990FXA-UD3 motherboard with:
North Bridge: AMD 990FX
South Bridge: AMD SB950
It has 14 USB 2.0 ports and 4 USB 3.0 ports:
AMD SB950 - 14 USB 2.0 ports
Etron EJ168 - 2 USB 3.0 ports
Etron EJ168 - 2 USB 3.0 ports
