Both Olympus E-M5 II and Fujifilm X-T1 IR have 16.0 MP resolution sensors but Olympus E-M5 II's sensor is Four Thirds (17.3 x 13 mm ) and Fujifilm X-T1 IR's sensor is APS-C (23.6 x 15.6 mm ).
Since Fujifilm X-T1 IR'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.
Another difference between these two cameras is that Fujifilm X-T1 IR'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 E-M5 II and X-T1 IR sensor size comparison.
As seen above, Fujifilm X-T1 IR 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.