Since most of my fleet has plastic wheels, I would like to change them to metal wheels soon. But, last time I was at my LHS, I noticed that Atlas sells two different wheel diameters, 33" and 36". I was woundering which wheel size is more prototypical, or do different sizes go to different cars.
No you would not want to put 36" wheels on all, you would want to use the appropriate wheel for the appropriate car. Also many of them are designed with the proper wheel diameter in mind so the coupler heights are correct with the proper wheel.