I like to think of it as when you change desktops by swiping, you're virtually grabbing hold of the desktop surface with the mouse and flinging it to the side. Likewise for "natural" scrolling -- we're basically grabbing hold of the window
content and flinging it (a la iOS). I still can't get used to "natural" scrolling after having done it the "unnatural" way for so many years -- my brain is trained to move the
scrollbar up or down, not the content.
The Kinect Hub on Xbox 360 works the same way, though that thing shows a little hand cursor that "grabs" the screen allowing you to fling it like a page in a book or something. The visual cue helps there and makes it feel natural.
All that said I agree there should be (more) options to modify the swiping behavior. Perhaps in a later update there will be. I also agree with you to an extent on the Mission Control perspective: if you're looking at the line of desktops at the top it makes sense to swipe right to move the
focus to the right, rather than the desktop itself. It's the GUI object our brains think we're actually moving when we swipe that causes this confusions. If we all agree that we're basically grabbing the desktop w/ the mouse and shoving it to the side (left) then all is good but clearly we don't all agree and need more options!
