BTW, I'd like to point out that Nuke the Fridge
(who was VERY reliable with Man of Steel news, even getting some set videos from the desert scene) reported back in May that WB was considering Lex Luthor and The Joker as the villains of JLA, with the possible logline being:
Lex Luthor creates and then unleashes a genetically engineered monster on Batman’s protectorate Gotham City. In the process, the Joker takes control of the creature in order to wreak havoc on the city and Batman.
But of course, now that we know Batman will feature in MOS2, this story (which officials are said to be very fond of) may have actually been for Man of Steel 2, rather than JLA.