Both Nikon S9900 and Fujifilm X-E2S have 16.0 MP resolution sensors but Nikon S9900's sensor is 1/2.3' (6.17 x 4.55 mm ) and Fujifilm X-E2S's sensor is APS-C (23.6 x 15.6 mm ).
Since Fujifilm X-E2S'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 S9900.
One other difference between these two cameras that is worth mentioning is that Fujifilm X-E2S'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 S9900 and X-E2S sensor size comparison.
As seen above, Fujifilm X-E2S has a 13.1x Larger sensor area than Nikon S9900. 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.