Re: Villains in the reboot series
I'd be very tempted to go for the Court of Owls in the reboot. If not though I'd go with the Riddler and have him trying to figure out the Batman's identity (who would be in his second year if crime fighting).
I would mind if they went for the Prey storyline with Hugo Strange, for those who've read it Batman hasn't been in action longer than about 6 months or so, he's very much still a rookie.
MAN OF STEEL
THE GREATEST COMIC BOOK MOVIE OF ALL-TIME