When you use beadboard wainscoting to remodel a room, you can get unfinished wainscoting that can be painted any color you would like. Paneling tends to come with a covering that gives it color and a look to it. Paneling, for the most part, is not designed to be painted.
People purchase paneling with designs and patterns already on it. Trying to paint over the slick paneling surface can also prove to be frustrating. Even the use of primer does not help paint stick to the slick surface of paneling. If you want to create a rustic look to your home but be able to paint your wall covering, then consider using wainscoting.