Fujifilm X-Pro3 has a 26.0MP APS-C (23.5 x 15.6 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor. On the other hand, Canon M6 has a 24.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features Digic 7 processor.
Another difference between these two cameras is that Fujifilm X-Pro3's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the X-Pro3 and M6 sensor size comparison.
As seen above, Fujifilm X-Pro3 has a 1.1x Larger sensor area than Canon M6. 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.