If this is implemented in the R1, then it would help to define the "groundbreaking" new AF system, as Maximilian mentioned. Since each "quad pixel" would have to cover more area than a "dual pixel" for all the circuitry then I could see the R1 coming in at the 20+MQP (where a pixel is a quad pixel) which is ideal for 4K video as well as plenty for professional stills use. It wouldn't surprise me if the marketing department then decides to call this a "80MQP" sensor and asks the programmers to come up with a new Bayer decoding (up-res'ing) to get 80MP to display & advertise.
Just keep in mind that the IQ and dynamic range will be affected by the increased circuitry on the sensor if that circuitry blocks more of the total light sensed by the sensor. And more false artifacts will occur if the Bayer decoding shifts from 4 cells (RGBG) to 16 cells(RRRRGGGGBBBBGGGG) - but I don't think the marketing department will mention that!
You know, at some point there's going to be so much circuitry and high resolution that I can see Canon finally coming out with a BSI (back-side illuminated) version of their sensors. That's really the only way to keep getting more complexity and resolution and image quality in a FF sensor as you approach the limits of what a non-BSI sensor can do. We may be seeing Canon's first BSI introduction, which would be quite an announcement in itself! Do I think this will happen in the R1? - No, but it sure wouldn't surprise me. And if they want to get a 45M QP sensor and beyond then I think they may be forced to use BSI in the future.