I have had the 12.9 Pro since a few weeks after it's launch, I remember it was pretty difficult to find at Apple Stores when it launched, the pencil and keyboard were out of stock for months.
Anyway, I picked up the 9.7 Pro about two weeks ago and I can't decide which one to keep! I have until tomorrow to return the 9.7 (14 day return policy at Store), but I can't decide.
9.7: Love the form factor, more portable, easier to use/handle while on the couch or in bed. The apple cases/covers in multiple colors are fun. Just as fast and loud (speakers) as the 12.9. Playing games is a very nice experience, as most require you hold the iPad and it's much lighter, and the smaller display makes it easier to interact with. Multitasking is not as good, since it's smaller so I find that I don't use that function as often, and almost never use two apps full screen because it's simply not big enough. The Apple Smart Keyboard is rather small, the keys cramped for me, I don't enjoy using it as much as the larger 12.9 full keyboard option.
12.9: Large immersive display, loud speakers. Great for watching content like Hulu and Netflix. Multitasking is great, even when using two full screen apps, almost like having two iPad Pros in portrait mode. Any time multitasking is used, it's a much better experience than the 9.7. The Smart Keyboard is much easier to use, same as the Apple Bluetooth keyboard, meaning it's full size. The 12.9 its BIG, and it's a little hard to hold for extended periods of time, one handed can be done for like 30 seconds before it becomes uncomfortable. It almost gravitates toward a desk or table or your lap to be used in that way, rather than being held like a tablet. It's can be difficult to hold for long periods when reading iBooks for example. Playing games is a little difficult for the same reason, but games look amazing. Having to move your thumbs around the bigger screen isn't always easy. Not many Apple accessories.
I could keep both, but I've never had more than one iPad, so I don't know that I can do that.
Send help.