The biggest difference between the 12.9-inch iPad Pro and 9.7-inch iPad Pro is really just size and a few camera specs. The larger model is equipped with a 12.9-inch (diagonal) Retina display with 2732‑by‑2048 resolution (264 ppi), and the smaller version ships with a 9.7-inch (diagonal) Retina display with 2048‑by‑1536 resolution (264 ppi). The 9.7-inch version also weighs less at 0.96 pounds, compared to 1.57 pounds.
The 9.7-inch iPad Pro is equipped with an upgraded 12MP iSight camera with Live Photos support, True Tone flash and 4K HD video recording capabilities. The 12.9-inch iPad Pro only features an 8MP camera with 1080p HD video recording. On the front side the smaller iPad Pro sports a 5MP FaceTime HD Camera, which is a significant upgrade compared to the 1.2MP FaceTime HD Camera found on the 12.9-inch iPad Pro model.
Both iPad models are powered by the same A9X chip and M9 coprocessor with Apple Pay, always-on Siri and Apple Pencil support. The 9.7-inch iPad also includes a Smart Connector for use with Apple's Smart Keyboard, just like its larger counterpart.