Both Nikon S6500 and Fujifilm X100S have 16.0 MP resolution sensors but Nikon S6500's sensor is 1/2.3-inch (6.17 x 4.55 mm ) and Fujifilm X100S's sensor is APS-C (23.6 x 15.8 mm ).
Since Fujifilm X100S's has a larger sensor area with the same resolution, this means that it also has a larger pixel area hence better light collecting capacity for a given aperture compared to Nikon S6500.
One other difference between these two cameras that is worth mentioning is that Fujifilm X100S'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 moire occurring in certain scenes.
Below you can see the S6500 and X100S sensor size comparison.
As seen above, Fujifilm X100S has a 13.3x Larger sensor area than Nikon S6500. 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.