I think two things work against this.
1. There is no Intel Chipset available yet that has an integrated USB 3.0 host controller and I don't see Apple putting in the one chip that was just barely released for USB 3.0 host control on these machines.
Intel doesn't support firewire 800 either and it is present. NEC and others have a PCI-e 1x host chip could use. Could put 1 maybe 2 USB 3.0 ports but still would be USB 2.0 port(s) present.
By the way, Nvidia, not Intel, provides the chipset for most of Apple's line up.
2. Apple seems to have a stake in bypassing USB 3.0 and going right to Light Peak late next year which has data rates that humble the new USB spec.
I think you fail to understand the purpose of Light Peak. Light Peak is just the latest in Apple's flirtations with its 'war' against cable 'clutter'. Remember Apple's proprietary video connector that ran video/usb over one connector between a Mac and the external monitor. Same essential problem. Want a single cable to connect two devices which have multiple communication protocols and/or channels to ship to each other.
In short, it is a multiplex/de-multiplex solution. It is also designed to be hot pluggable which would make it a leap over what "expresscard" offers.
However, this is NOT going to be a general replacement for USB.
1. Your average mouse/keyboard/USB flash drive/etc. have zero need for some complicated, more expensive, multiple protocol connection. Really? you need a 10gb/s link to your mouse????
2. An optical link isn't going to supply power. So that makes bus powered hard drives. They are thinking of coupling in a copper wire to provide juice but is likely going to conflict with the longer lengths they are talking of. However, now getting to the point where throwing the kitchen sink at the port.
If you have a USB device and the plug fits into the USB port you can be pretty sure the devices can talk to one another.
Light Peak is different. Unless they make all the possible protocols manditory than you could have Light Peak hubs that can't talk to other more lmited Light Peak Hubs. That's is fine for limited use connectors. However, that runs counter to true "plug and play".
3. There is some overlap with the upper range of USB 3.0 and Light Peak for modern storage transfer. However, that is a narrow niche which USB 3.0 hasn't really fully exploited .... yet.