Fujifilm Z900EXR has a 16.0MP 1/2" (6.4 x 4.8 mm ) sized EXRCMOS sensor and features EXR 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 8MP more than Fujifilm Z900EXR'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 Z900EXR and M3 sensor size comparison.
As seen above, Canon M3 has a 10.8x Larger sensor area than Fujifilm Z900EXR. 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.