Fujifilm XQ2 has a 12.0MP 2/3" (8.8 x 6.6 mm ) sized CMOS sensor and features EXR Processor II processor. On the other hand, Canon M3 has a 24.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features DIGIC 6 processor. Canon M3's sensor provides 12MP more than Fujifilm XQ2'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 XQ2 and M3 sensor size comparison.
As seen above, Canon M3 has a 5.7x Larger sensor area than Fujifilm XQ2. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.