These are the funny omissions in the otherwise ‘Pro’ hardware. When you call something pro, your expectations are reasonably inflated to have high-end internals. There is a bitter taste for buyers here, where there isn’t just one device where you can get everything that’s new in iOS hardware.
I think super-fast Touch ID isn’t in the Pro for supply-chain reasons. Producing Touch ID sensors has always been a bottleneck for Apple so I’m pretty sure this is the case here. They need every sensor they can get for the millions of iPhone 6s produced every day, so the other devices have to suffer with the scraps and use the first-generation sensors. Note also that the new iPad mini also uses the older Touch ID.
Regarding the lack of 3D Touch in the iPad Pro, I think there’s several factors that add up to Apple skipping it for the first generation. Some of the reasoning is purely qualitative assertions about user experience; ergonomically ramming your finger into something you hold in your lap is nowhere near as satisfying as a phone that you can hold steady upright.
At a technical level, I think adding the 3D Touch force sensors to an iPad Pro is much more complicated than adding it to an iPhone. Why? Because on the iPad Pro, the screen technology is very different due to the need to detect electromagnetic pulses for the Apple Pencil. There are very thin margins in which to fit such components and perhaps it’s technically impossible to add both 3D Touch and Pencil support with Apple’s current engineering methods.
Finally, the omission of 3D Touch is great for product differentiation. The iPhone 6s is all about 3D Touch, every ad mentions how Peek and Pop can change the way you do things on the phone. Frankly, the iPhone is Apple’s flagship product so it almost needs to be ‘more advanced’ than its siblings in some way. Meanwhile, the iPad Pro is marketed along different axes — namely Power and the creative drawing potential of the Apple Pencil. Throwing 3D Touch into the mix alongside the Pencil, which does indeed track pressure but for a whole different purpose, would surely confuse the messaging.