Sometimes you want the specular map to be quite different than simply a desaturated diffuse. For example, if you're making scratches on metal, you would probably want the scratches to be dark in the diffuse but bright in the specular.
Another example would be grime and dirt, which you would want to darken on the specular separate from the rest of the texture.
Another example would be grime and dirt, which you would want to darken on the specular separate from the rest of the texture.