Maybe they had to cut prices somewhere? Yes, but I think you are right. I looked up the Prototype, and it was overall the same controller, with just even better build quality. I would not be surprised if the final design of the smaller B button was chosen to save costs.
It is really crazy that people (like us) are still talking about the controller, because back in the day I remember the debates being positive and negative. I remember people slamming Nintendo for designing a controller again that only fits Nintendo's needs and not 3rd parties. A controller that will be horrible for several genres of games. Then I remember those praising the controller as the best controller designed and would undoubted change the future on controllers.
It is surprising, that Nintendo went such a drastically different direction with the Wii. The Wii Classic Controller was only designed to really play Virtual console games, but I think they could have made a Nintendo Pro Controller that generation that was the Gamecube Controller.