If the breakfast downstairs is that much better to you, I fail to see why it should make no real difference to the hotel... clearly they think that they can charge much more for it.

Welcome to Tokyo.... meals are ridiculously expensive. $40 for breakfast is insane, agreed, but it is not unusual for Tokyo hotels (or many Tokyo restaurants). I doubt Hilton will feel compelled to do much for you. The best you might be able to do is get downgraded to a normal room and maybe get comped breakfast then....