It's a piss poor design decision by Nintendo. My 3DS has scratches as well, and while they disappear if I rub them, they get more obvious by the day, and it's quite annoying. And the worst thing? 3DS XL has the same exact problem, even after it caused a controversy with the original. Get your **** together, Nintendo.
Good god I might stick with Wii U only or get a PC next gen if Sony is doing the same. I'm done with Microsoft's awful practices.