Eh, the 12.9 inch has double the RAM. 9.7 inch just has true tone. I'd probably pick the 12.9 inch if I bought right now (But I'm waiting for the second gen).Not gonna happen. Look at the 9.7" iPad Pro, already a superior device than its same-gen brother.
That said, it's looking more and more that the 5.5 inch phone is going to be significantly better than the 4.7 inch phone. Disappointing for sure.