For most scientific applications, a monochrome CCD is the best choice for several reasons. First of all, you have control over the filter sets used. You may want to change from RGB to CMY to photometry filters or narrow band filters. A color CCD has a fixed set of filters, typically in a Bayer pattern (red-green-green-blue). If you use a blue filter in front of a color CCD, only one of 4 pixels will see any significant amount of light. Color CCDs can deliver a color image in a single shot, but they compromise spatial sampling. A 10 megapixel color sensor is not delivering 10 megapixels of red, and 10 megapixels of green, and 10 megapixels of blue. A monochrome sensor acquiring a red, green, and blue image using a filter wheel acquires 10 megapixels of each. Typically you cannot bin color CCDs (you can, but the results will have limited utility).