Sigma DP2 Quattro has a 20.0MP APS-C (23.5 x 15.7 mm ) sized CMOS (Foveon X3) sensor and features TRUE III engine processor. On the other hand, Sigma DP3 Merrill has a 15.0MP APS-C (24 x 16 mm ) sized CMOS (Foveon X3) sensor and features Dual TRUE II engine processor.
Sigma DP2 Quattro's sensor provides 5MP more than Sigma DP3 Merrill'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.
Below you can see the DP2 Quattro and DP3 Merrill sensor size comparison.
Sigma DP2 Quattro and Sigma DP3 Merrill have almost the same sensor size so none of them has any significant advantage over other in providing control over depth of field when used with same focal length and aperture.