Fujifilm X-E2S has a 16.0MP APS-C (23.6 x 15.6 mm ) sized CMOS X-TRANS II sensor and features EXR Processor II processor. On the other hand, Fujifilm X-E3 has a 24.0MP APS-C (23.6 x 15.6 mm ) sized CMOS X-TRANS III sensor and features EXR Processor III processor. Fujifilm X-E3's sensor provides 8MP more than Fujifilm X-E2S'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 similarity between these two cameras is that both Fujifilm X-E3 and Fujifilm X-E2S sensors lack anti-alias (Low-Pass) filters. 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-E2S and X-E3 sensor size comparison.
Fujifilm X-E2S and Fujifilm X-E3 have sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Fujifilm X-E2S has 50% larger pixel area compared to Fujifilm X-E3, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.