So, the battery capacity itself is actually a tiny bit better than the Air 2 (27.5 Wh vs 27.3 Wh). What I wonder though, is how the new display will affect battery life. One of the benefits was supposed to be the ability to adjust the refresh rate dynamically to save power, which the 9.7" will have as well. But it may wind up being a bit of a wash with other things pulling at the battery now that weren't there before (extra speakers, extra screen brightness).
That said, the clock speed on the 9.7" isn't that much slower than the 12.9". It may have fewer GPU cores though in exchange. The CPU numbers Apple's reporting suggest a minor downclock. It's closer to the 12.9" Pro than the 6S, I'd guess maybe around 2-2.1Ghz instead of 2.2Ghz?. That said, the GPU numbers are strangely different. I'd guess that perhaps these are A9Xs that are binned with one disabled GPU cluster pair (The A9X has 12 clusters, in pairs of two). Having one disabled cluster pair for 10 clusters instead of 12 would explain the discrepancy of the GPU numbers. But yes, these are very likely just the same A9Xs as are used in the 12.9" Pro, just binned. That doesn't surprise me all that much, really. A smaller difference than what you get between the 13" and 15" MBPs, honestly.