Of the 12 pins, two are grounds (you really only need one), one is for orientation detection and two are for usb 2.0 support. Lighting has 8 pins plus a ground ( for reference USB 3.0 has 8 pins plus two grounds) and is an active cable, so it doesn't need separate pins for legacy support. It's not as straightforward an argument has USB 3.0, but lightning could handle USB 3.1 functions, possible with the exception of the increased power (which is irrelevant to a phone).
We'll see what happens, but I suspect they'll continue to use lightning on phones. It's "thinner", could be upgraded to USB 3.0 if not USB 3.1, and gives them control of the ecosystem.