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I find it hard to believe that the device came to you scratched. Especially in a sealed package. I can understand the back if enough stuff got in, but not the way it was sealed. The screen is extremely hard to scratch since it's glass. Unless you play with iron filings at home or took it to the beach, it really can't be scratched. Unless you carry diamonds in your pockets XD
There are ways to sync music to the iPod without iTunes, they are third party though. I know the stock music player on Unbuntu can do this (since it doesn't have a version of iTunes). There are others as well. Purchasing and having apps can be done through the iPod and iCloud for backup. Yes, there are limitations, but you aren't entirely tethered to iTunes any longer.
I'll agree that the back is easily scratched (a little too easy). The front, well, like I said, unless you play with iron filings on the screen and rub them in, carry diamonds in your pocket (or intentionally scratch the screen with it), or play in sand, it's not going to scratch. It's most likely a grease or oil stain (use damp cloth to rub it out).