Canon 1D X II has a 20.0MP Full frame (36 x 24 mm ) sized CMOS sensor and features Dual DIGIC 6+ processor. On the other hand, Nikon D3X has a 25.0MP Full frame (35.9 x 24 mm ) sized CMOS sensor and features Expeed processor. Nikon D3X's sensor provides 5MP more than Canon 1D X II's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Below you can see the 1D X MII and D3X sensor size comparison.
Canon 1D X II and Nikon D3X have almost the same sensor size so none of them has any significant advantage over other in providing control over depth of field when used with same focal length and aperture.