It used to be that people chose the Commander for its aluminum frame (versus the steel frame of the 5" gun). Now I think it comes down to subjective things like feel and balance in the hand. I prefer the balance of a steel-framed "Combat" Commander to a 5" Government Model, for example. I also like the quicker cycling of the shorter gun.
Against that is the (usually) greater reliability and longer sight radius of the 5" pistol.