"Image quality" seems to be the most common answer... It eliminates the need for color filter deposited on the sensor, and also seem to require cares taken in lens design to have optical parameters converged for all three image planes in respective wavelengths(can't have one color being magnified or out of focus than others).

I suppose whether those points are pros or cons depends on design/manufacturing capability, and considering rarity of modern 3CCD designs, likely decisions are difficulties outweigh advantages today.