Well I do not think the 9.7" is better.
Screen Resolution
The 12.9" has a larger screen resolution and for apps that support it gives the 12.9" additional screen estate.
RAM
The 12.9" has 4GB RAM whereas the 9.7" has only 2GB.
Processor
Whilst both devices share the AX9; on the iPad comparison page, Apple lists the specs of the A9X in both of the iPad Pros, comparing them to the A7 chip in the iPad Air, iPad mini 2/3, and iPhone 5s. The 12.9-inch iPad Pro lists a 2.5x faster CPU and 5x faster graphics, while the 9.7-inch iPad Pro lists a 2.4x faster CPU and 4.3x faster graphics.
Speakers
Have you heard the sound from the 4 speakers on the 12.9" Pro, awesome.