Yup, just call Nintendo and complain about the top screen scratches. I bet they will offer to repair or replace it for free. I'm considering doing the same thing... I got a used Zelda 3DS, and it had the top screen scratches, plus the left side of the d-pad is "creaky" (hard to press sometimes). You can also complain about "paint bubbles" if your system has any - that got me a DS Lite replaced once.
As for 3DS XL deals, there's just that blue one with MK7 pre-installed... I think the best we might get here in the US (anytime soon) is a solid black system. There could be a bundle for the next 3DS Zelda game, but that's at least 1-2 years away.
Let me know how it goes! Good luck.