Do you know that 5V is a fixed part of the spec or are you just guessing? There's also a lot of speculation that lightning is very dynamic and could allow power to be carried over several pins, not just one pair. I also don't think any extra pins would be needed to implement usb3 since the lightning connector wasn't trying to maintain physical compatibility with usb 2.0.
It is an educated guess. Things like voltage are messy. Variable voltage needs to be managed well, which means more complexity to something that is already complex. USB PD requires a negotiation handshake and circuitry to handle the variable voltage. Neither of these reside in the cable, and so you
tend to need cables built for whatever current this might wind up entailing.
But here's the thing, let's assume I am 100% wrong and Apple can push 12V on the pin in a similar way. Hooking up more voltage to a 3.3V battery
does nothing for your charge speed. Charge speed is entirely determined by current. So if you've upped the voltage, but still can't move more than 2.4A across the wire because the wire is too thin to carry more, you've fiddled with things for zero gain. Input voltage is determined by the battery voltage you want to charge. 12V on USB C is important because laptop batteries tend to be ~8-11V to run the 5V circuitry. ARM gets away with 3.3V which is more flexible in mobile devices.
The other problem is that yes you do need more pins for USB3 (and the iPad Pro
has them). Data speed is a mix of a couple things:
1) How many pins you have for data (each pin transmits one bit per clock cycle)
2) How fast your clock is
And contrary to what a lot of non-engineers tend to believe, you can't just push the clock speed over the wire higher and higher. You get more and more noise that screws up your signal, crosstalk, and other fun things because fast moving electrons generate magnetic fields that then mess up how other fast moving electrons travel. So to get the sort of data USB3 pushes, they had to add more pins to carry data. That reversible USB C connector? USB 3 uses
both sides. And if lightning wants to carry USB3 over it, it is going to need to do one of two things:
1) Use both sides of the plug to double the pin count.
2) Use an expensive active cable where it converts USB 3 into something proprietary, running at a higher clock speed with fewer pins to talk with the iPad itself.
And if you look inside the lightning port on the iPad Pro, and compare it to the Air 2, the Pro has connections for both sides of the lightning cable, while the Air 2 only has connections for one side. So it's pretty clear Apple went with #1.
