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.
THE BAT IS DEAD, BURY IT... CONSIDER THIS MERCY
SUPERMAN TO BATMAN (BATMAN V SUPERMAN: DAWN OF JUSTICE)