Quality of color and dynamic range are paramount, but megapixels is also very important for some applications. The D800 seems to be the one to beat in all categories at the moment. I am buying one for architectural and landscape work until Canon makes a similar high MP body. If they don't, then I will probably move back to Nikon for all my work, just to keep from carrying two systems with me on jobs.
I think Canon dropped the ball and got too sidetracked with video. But maybe that's where the money is from a corporate standpoint.