Both Canon M6 and Fujifilm X-E3 have APS-C sized 24.0 MP resolution sensors so sensor size and resolution is not a differentiator between these two cameras.
One other difference between these two cameras that is worth mentioning is that Fujifilm X-E3's sensor doesn't have an 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 moiré occurring in certain scenes.
Below you can see the M6 and X-E3 sensor size comparison.
As seen above, Fujifilm X-E3 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.