Due to the way USB 3.0 is implemented, the USB implementers forum no longer recommends the use of companion controllers which significantly reduces backward compatibility with older OSes. With USB 2.0, the EHCI controller was simply added as an additional PCI function to the existing device. This approach allowed older OSes to use the controller in USB 1.1 mode if a newer USB 2.0 driver wasn't loaded. With USB 3.0, the ports are completely non-functional without an XHCI driver loaded to run them. Windows 7 doesn't natively support XHCI which means that any USB devices like keyboards, mice, and internal devices attached to the USB bus wouldn't function before the drivers are loaded. This would prevent setup from completing on a system with only USB 3.0 ports.
USB 3.0 needs a new chipset with it built in(or a 3rd party controller). It is like when USB2 came out and all boards still had USB 1.1. Motherboard makers filled the void by adding 2-4 ports with 3rd party controllers.
As time goes on, USB 3.0 will replace all ports.
USB3 is fully backwards compatible, it is just a matter of cost(controllers add to the cost while usb 2.0 is a part of the chipset so effectively free).