Both FujiFilm S1600 and Nikon D90 have 12.0 MP resolution sensors but FujiFilm S1600's sensor is 1/2.3-inch (6.17 x 4.55 mm ) and Nikon D90's sensor is APS-C (23.6 x 15.8 mm ).
Since Nikon D90'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 FujiFilm S1600.
Below you can see the S1600 and D90 sensor size comparison.
As seen above, Nikon D90 has a 13.3x Larger sensor area than FujiFilm S1600. 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.