The 9.7" is fine for taking notes... Mine is an Air 2, so it would be even better with the new one, using the Pencil. I also have a 12.9" Pro, and often take notes on it in split screen, with email or other apps on the other side. When I used to use paper notebooks at work, I preferred the smaller memo-pad sized ones anyway.
Sure, you can fit a lot on a page with the 12.9, but scrolling is easy, and with a tablet, you have near infinite pages in your notebook. I really like the 12.9 for some things, but I wouldn't carry it around the office like info with the 9.7. The difference in weight is very noticeable, and it's tough to one-hand the big one. I usually balance it on my forearm if I have to use it standing up.
It's great having both, but if I had to downsize my fleet, I'd probably carry a 12" MacBook and a 9.7" iPad.