Both Fujifilm X-T1 and Olympus E-M5 II have 16.0 MP resolution sensors but Fujifilm X-T1's sensor is APS-C (23.6 x 15.6 mm ) and Olympus E-M5 II's sensor is Four Thirds (17.3 x 13 mm ).
Since Fujifilm X-T1'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 Olympus E-M5 II.
Below you can see the X-T1 and E-M5 II sensor size comparison.
As seen above, Fujifilm X-T1 has a 1.6x Larger sensor area than Olympus E-M5 II. 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.