I think with so much experience missing from the squad c.f. the RWC team, the challenge for Cheika is to balance the experience he has at hand with the up and coming talent. For this reason players like Moore, Fardy and Kuridrani, and to a lesser extent Foley, To'omua, Horne etc are crucial to the core of the team despite their perceived lack of form. I think this has been most evident in the second row department and it won't surprise me in the slightest if it emerges that it was always his intention to try a different combination in each game.
Remember the Bledisloes last year? Despite winning the first game Cheika completely changed it up for the second because he already had a plan to do that because he needed to try out everyone, the RWC was the end goal, losing the 2nd Bledisloe was collateral damage.
I think the end goal here is actually the Bledisloe. Granted, he probably wasn't expecting to lose the series to the Poms on the way through, but ultimately he is still sorting through his options. Losing all of Beale, To'omua, Tomane, Pocock, McCalman, etc at some point prior to or during the series no doubt upset his plans more than a little too.