The only down side to this is public information on the chip sets that will hit the devices. Right now Apple is rolling out the Haswell in the MacBooks, and people already know to expect significant battery life increases and other standards to increase significantly...but they only know it because Intel doesn't really have any reason to keep this stuff from the public, they make it and tell the world, and then the consumer expects it.
With this "in house" fabrication and development, Apple can essentially slowly roll the features out to their own schedule because who will know what is coming down the pipeline? It's in house so they can say "Well this version will have "X"...when really, it could do "X" and "Y"...", but they'll wait until the mid generation refresh is due before they roll that function out.
Not trying to sound pessimistic, hopefully this allows them to lower cost a bit over all...and maybe it will give them more opportunity to have a higher performance setup that the other manufacturers don't because they'll continue to use outside developed components.