I just realized the significance of the TARDIS redesign; the TARDIS throughout seasons 1-4 was weathered, looking somewhat battered still from the war, representing how The Doctor himself was still suffering from the trauma of the time war; the season 5 TARDIS is resplendent and pristine, because the 11th Doctor is far more recovered from the trauma, latter dismissing the war as a 'bad day'.
The Atraxi jailkeeper states that no one who ever lived on earth is guilty of any of the crimes that their race police. That means they don't care about anything humans have ever done, including infamous acts such as attempted genocide. (At least on a planetary scale.) Prisoner Zero must have done something exceptionally terrible for them to give it that title.
Maybe not. Unlike the Judoon, who are pretty much hired guns, the Atraxi may only care about stuff done to them or within their jurisdiction. Besides, while ignorance of the law is not an excuse, it can only be enforced if the perpetrator could have reasonably known the law in question. The Atraxi had never had contact with humans, so how are humans supposed to know their laws?
Prisoner Zero takes Amy's form because the phone the Doctor used to write the virus on had pictures of all its forms. The phone was Rory's. Rory is Amy's boyfriend, more or less. Are there no pictures of her on the phone? He's never taken a silly selfie with her or snapped a picture when she's not looking?
Actually, it takes the form of Amelia (with her imaginary friend, or whatever she's dreaming of at the time). Rory's phone probably isn't old enough for him to have made pictures of Amelia with it, he's also unlikely to have thought of photographing the Doctor. Still, this raises a question - does Prisoner Zero take the form of a person the way they look now, or the way they see themselves? The mother with kids and the man with a dog suggest the latter possibility. Which would mean Amy still thinks of herself as a child.
