Question: Except for Two-Face, Killer Croc, Scarecrow and Jervis Tetch, why were the rest of the villains redesigned?
Answer: Probably because different people were working on the game. Scarecrow and Croc also have different looks if you've played Asylum, City, and Origins, they look different here too.
Question: How can the stout Prof Pyg place all those bodies without being noticed, and why does he do this? Why not just throw them into the nearby ocean?
New this monthAnswer: He might have used his disguised dollotrons to place the bodies or simply disguised himself when he sneaked out. As Gotham is in a criminal turmoil and most of the streets are dark and empty, it wouldn't be that hard to move around in the shady alleys unnoticed. And why did he? Simply because he's insane. An obsessed, maniac psycho—and sociopath. Placing the bodies like that is part of his "artwork."
Question: Were there any hints Jason was the Arkham Knight?
Answer: Besides all of the subtle hints that point to Jason being the Arkham Knight, the audio files that are available have the Arkham Knight revealing his identity as Jason to Barbara.
Answer: Quite a few. To name a couple: the scene in the diner shows a man wearing a red hoodie with an "A" chalked onto the table in front of him; this is Todd, a reference to the red hoodie he wore, with the "A" hinting at his identity as the Arkham Knight. It's also foreshadowed in several lines of the AK's dialogue, including yelling at Batman: "How long did you take before replacing me? A month? A week? I trusted you and you just left me to die!" Finally, in Batman's vision of Joker's misdeeds, one of them is Todd's apparent death, titled "Remember the New Guy?"
Answer: No.
Question: How could Batman be infected if he cured himself of the Joker's poisoned blood in Arkham City?
Answer: He was exposed to a toxin bomb, so he probably got a bigger dose of the fear toxin.
The fear toxin only makes a person see their worst fear. It doesn't make them physically transform into it.
Answer: He was exposed to the fear toxin when it was unleashed on Gotham City.
How does that explain him being still being infected? The four people he had at Panessa studios were infected by a blood transfusion but Batman cured himself of his. Plus, the fear toxin only makes a person see their worst fear.
Answer: He was infected through a blood transfusion.
The Joker infected Batman with a blood infusion in Arkham City but Batman cured himself so, it would make no sense for him to still be infected.
Question: Just where did the militia get the money for all their weapons and gear? The only rogue who's got good money is The Penguin, and he doesn't seem capable of necessarily funding a whole army.
Answer: All the villains financed the Arkham Knight: Penguin, Two Face, Harley, Scarecrow. This is why Two-Face and Penguin stayed in Gotham and risked getting gassed to rob banks and run guns; they'd dangerously low on funds.
Answer: The Arkham Knight is behind the whole thing. He probably financed it somehow. Given who he turns out to be, probably from stolen drug money.
Answer: As a child, Jervis Tetch never had any friends. Even in his adult years, he was all alone. When Jervis asked Batman to be his Alice, he was essentially asking Batman to be his friend.