Hey so I was just agonizing over this decision for weeks and just bought the 11 inch 64 gb pro. Check on Amazon, as I got it for $100 off which is extremely rare for apple products, I think it was a father's day sale.
I was mostly deciding between the sizes because I knew that I would get 64 gb because I'll be backing everything up to icloud and 64 gb is more than enough for local working storage.
At first, I was leaning toward the 12.9 as common convention goes, bigger is better and I thought multitasking would be much better on the larger screen. However, when I got to the apple store and compared them both, the 12.9 was way too big too be comfortable for a tablet. You can't really grasp it well with one hand and write with the other. And I'm 6'1 with big hands. The 11 inch felt so much more comfortable to hold and carry. Additionally, I tested the 11 inch screen with multiple apps open side to side (textbook and notability or youtube and notability) and there is plenty of screen space to do what you need.