Their latest stacking GPU patents show the way: Stack the cache under the CPU, not above it. The cache chips themselves do not produce much heat (as a process optimized for cache will be very low leakage, and only small areas of the cache are actively switching at any given moment), the problem with current stacked products is that the cache is between the active die and the heatsink.

The reason they didn't do it in the right order to start with is that the top die cannot be designed to work both with and without the cache. They can only start stacking the cache below the cpu once they accept that every single product will have a stacked cache.