TheDane :
For most current sensors higher pixel count is to be preferred since you then have both options - greater resolution in good light and less noise (when downsampled) in low light.
Between two sensors of otherwise identical construction quality, the larger cells have multiple advantages:
- lower proportion of sensor area lost to cell wiring and partitions, which reduces the proportion of lost light and effects of minor sensor imperfections
- larger cell area, which makes it easier to couple light into it and in turn improves sensitivity for low light and fast shutter situations
- higher cell capacitance, which makes individual cells less noisy and gives them a broader dynamic range to simultaneously preserve more details in highlights and shadows - with small sensors, you easily end up with shadows getting washed out in bright scenes and highlights getting clipped to white from over-exposure; often in the same shot
While a higher resolution sensor does give better flexibility using shutter and image processing tricks like multiple exposures for digital integration, the sensor with larger cells would have better raw output quality and dynamic range for all those situations where relying on tricks to enhance image quality is not possible.