Nikon patent application 20130182173 is for combining/stacking a dedicated AF and imaging sensors without losing any light (in theory):
"The idea is simple: RGB color filter array does not use roughly 2/3 of the light in each pixel, why not use the lost light by a complementary-colored organic AF sensor stacked on top on the regular Bayer-pattern sensor."
From the patent application:
"A solid-state imaging device includes a second image sensor having an organic photoelectric conversion film transmitting a specific light, and a first image sensor which is stacked in layers on a same semiconductor substrate as that of the second image sensor and which receives the specific light having transmitted the second image sensor, in which a pixel for focus detection is provided in the second image sensor or the first image sensor. Therefore, an AF method can be realized independently of a pixel for imaging."