Mr. Freeze's condition will cause death if his body is exposed to above freezing temperatures. While an update to the game tried to correct the character's design by adding his helmet, Freeze's arms are still exposed, which would yield the same negative results.
Batman releases Superman from prison on the grounds that he is the only one who can stop Braniac. However, Batman never considers using his interdimensional device (used earlier to bring Black Canary and Green Arrow into this universe) to bring in the good Superman from the previous game.
Grodd states the Society has disbanded upon learning Brainiac's true plot. However, having psychic powers, Grodd could have easily mind controlled them to do his bidding, as he had with Black Canary and Green Arrow. Additionally, Grodd still holds the detonator for the bomb inside Deadshot's head, meaning he should still at least have leverage over the mercenary.