Fujifilm X-Pro1 has a
16.0MP APS-C (23.6 x 15.6 mm ) sized CMOS X-TRANS I sensor and features EXR Pro processor. On the other hand, Nikon D90 has a
12.0MP APS-C (23.6 x 15.8 mm ) sized CMOS sensor .
Another difference between these two cameras is that Fujifilm X-Pro1'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 moiré occurring in certain scenes.
Below you can see the X-Pro1 and D90 sensor size comparison.
Fujifilm X-Pro1 and Nikon D90 have almost the same sensor size, so neither of them has any significant advantage over the other in terms of providing control over depth of field when used with the same focal length and aperture.