The individual cores on the A9X SoC are significantly faster than the cores of the A8X. This basically means that 2 A9X cores can beat 3 A8X cores.
Because many workloads are not well threaded (don't take advantage of multiple cores) the faster single-core speed makes the A9X the better performer.
Though seemingly the A9X in the 9.7" Pro seems to throttle down faster and harder than the A8X Air 2 does. I've just been running the 3DMark Sling Shot Extreme test on both devices, and over 11 tests one after another the Pro has basically dropped 500 points where the Air 2 is only down 140. Something I wasn't expecting at all.
(Benchmark, no demo, wifi on, brightness 50%, volume at zero, true tone off, night shift off, auto brightness off)
Code:
Pro 9.7 Air 2
3088 1932
3027 1917
3050 1918
2862 1923
2929 1929
2768 1926
2670 1904
2741 1875
2621 1825
2716 1800
2600 1793
If I run the benchmark again, this time with the Demo on then I've seen the figure wobble about. First run had the Pro on 2392 (well below the average of 3037), where the Air 2 managed 1915 (just a little under its average of 2054).
I hadn't been looking for a reason to not keep the device, but now I'm a little unsure and certainly a bit disappointed.