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This shit happened to me recently, too, except the burglar broke into my apartment. I didn't even have my 3DS sitting out - it was in a drawer in my bedroom.
Not only did they take my 3DS and all my games, but they also took my fucking GBA, GBC, and all of those games. So I literally lost every pokemon I ever caught.
So I know how you feel, man. Shit fucking sucks, but we'll move on eventually.