Fujifilm X100 has a 12.0MP APS-C (23.6 x 15.8 mm ) sized CMOS sensor and features EXR processor. On the other hand, Leica X Vario has a 16.0MP APS-C (23.6 x 15.8 mm ) sized CMOS sensor .
Another difference between these two cameras is that Fujifilm X100'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 X100 and X Vario sensor size comparison.
Fujifilm X100 and Leica X Vario 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 X100 has 32% larger pixel area compared to Leica X Vario, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.