BIG DIFFERENCE IN CAMERAS
The 9.7-inch iPad Pro has a 12-megapixel iSight camera while the 12.9-inch iPad Pro has an 8-megapixel iSight camera. The 9.7-inch has True Tone Flash. The 12.9-inch has NO flash.
The 9.7-inch iPad Pro can do 4K video. The 12.9-inch iPad Pro can only do 1080p. The 9.7-inch has Cinematic Video Stabilization. The 12.9-inch does NOT.
The 9.7-inch iPad Pro's FaceTime HD Camera takes 5-megapixel photos with Retina Flash while the 12.9-inch iPad Pro's FaceTime Camera takes 1.2-megapixel photos (no Retina Flash).
For the complete list of differences between the back and front cameras, see the detailed comparison of iPad Pro specifications.
DIFFERENCES IN DISPLAY QUALITY
Apple added features such as 'Wide Color Gamut' and 'True Tone' to the 9.7-inch iPad Pro's display. Those features are lacking on the 12.9-inch iPad Pro.
DIFFERENCES IN MEMORY SIZE AND SPEED
The 9.7-inch iPad Pro has 2GB of RAM whereas the 12.9-inch iPad Pro has 4GB of RAM. This was not only confirmed with Geekbench testing, but the 12.9-inch iPad Pro's memory performance score is 28% better than the 9.7-inch iPad's memory score.
DIFFERENCES IN SPEED OF LIGHTNING CONNECTOR
If you are a professional photographer or videographer hoping to import your media from a 2000x SDHC/SDXC UHS-II memory card using an SDHC/SDXC UHS-II reader (U3, Class 10, 300MB/s max) connected to the Lightning connector of your iPad Pro, you will want to order Apple's Lightning to USB 3 Camera Adapter. Why? For one thing, that reader requires the iPad Pro to be plugged into the charger.
However, the Product Overview for that adapter reveals a key deficiency in the 9.7-inch iPad Pro. To quote, "The 12.9-inch iPad Pro transfers data at USB 3 speeds, while the 9.7-inch iPad Pro uses USB 2." (UPDATE: We tested both iPad Pros. The 12.9-inch iPad Pro samples and previews our test photos 7 times faster and imports them 3 times faster.)
The differences discussed above may or may not affect your decision to buy the 9.7-inch iPad Pro, but we wanted you to press the BUY button with eyes WIDE open.
HOW DIFFERENT IS PERFORMANCE?
Check out our article comparing the CPU, memory, and GPU performance the 9.7-inch iPad Pro with the 12.9-inch iPad Pro, the iPad Air 2, and the iPhone 6s Plus.
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