This is really a question for Apple. System preferences allows you to set the scrolling direction for a mouse and the trackpad to either "natural" or unnatural, I suppose. But they tied the two together for some reason. So if you change it in one device, it automatically changes in the other device. And there doesn't seem to be anyway to disconnect them. I don't understand the thinking behind this other than maybe with the magic mouse, the scrolling motion is similar to that on the trackpad? I don't know because I've never used a magic mouse. But I'm using a third-party wheelmouse. While the "natural" direction does, in fact, seem natural for me on the trackpad -- it doesn't feel at all natural with the mouse wheel.
Please, Apple, disconnect these two settings and allow users to set them independently. Thank you.