Apple's core count decision looks to be based on the thermal clearance vs. the single core speed (which is the sensible approach). In other words the third core was added to the A8X because two cores would have left thermal overhead, which is leaving performance on the table.
A9X is already thermally constrained with two cores because each core is significantly more powerful than the A8X cores. Adding a third wouldn't have done anything useful, so it didn't happen.