Actually I suspect what would've worked even better was to make BOTH screens the same aspect ratio. A huge problem is how the bottom one is wideer than the top one so the borders will rub against the top, which with dust there would cause scratches but dust or no wouldn't be an issue if the frames hit where the screens ended anyway.
And for whatever it's worth I only really had the scratches show up once I started carrying it in my pocket, I abstained for quite while due to the size, but with the revamped street pass I figured I'd take it out more often again.