Fujifilm X-T2 has a 24.0MP APS-C (23.6 x 15.6 mm ) sized CMOS X-TRANS III sensor and features X-Processor Pro2 processor. On the other hand, Nikon S6900 has a 16.0MP 1/2.3' (6.17 x 4.55 mm ) sized CMOS sensor .
Fujifilm X-T2's sensor provides 8MP more than Nikon S6900's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Another difference between these two cameras is that Fujifilm X-T2'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-T2 and S6900 sensor size comparison.
As seen above, Fujifilm X-T2 has a 13.1x Larger sensor area than Nikon S6900. 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.