I would prefer a non downclocked A9x on the Air 3 and not having the new speakers
The stereo speakers are the main factor in why I'm jealous of the Pro, so in my opinion that's what would entice me to upgrade the most. That doesn't mean I'm not envious of the A9X.
Though it's not just battery life they have to consider but thermals too. Larger and thicker body of the Pro allows greater heat dissipation. It's quite likely that Apple will make the Air 3 even thinner, judging by their history.
Apple did say that the A9X was specifically designed for the 12.9" form factor. If they could plop it in an Air without even down clocking, it would prove that they a) were lying or b) did a lousy job of it. Either way, it would be extremely embarrassing for Apple and hurt the Pro severely. A 'professional' tablet with no more performance than its consumer orientated, much cheaper, much smaller sibling - laughable.
I definitely think the Air 3's SOC will be slightly down-clocked in comparison to the Pro. That's just my educated guess.