Both Fujifilm S2 Pro and Fujifilm S3 Pro have 6.0 MP resolution sensors but Fujifilm S2 Pro's sensor is APS-C (23 x 15.5 mm ) and Fujifilm S3 Pro's sensor is APS-C (23 x 15.5 mm ).
Since Fujifilm S3 Pro'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 Fujifilm S2 Pro.
Below you can see the S2 Pro and S3 Pro sensor size comparison.
Sensor Size and Resolution Comparison image of Fujifilm S2 Pro and Fujifilm S3 Pro Cameras
Fujifilm S2 Pro and Fujifilm S3 Pro have the same sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture.