Unfortunately, the natural choice is Luthor, but so many moviegoers would want something else for a change, at least for a start...even if the new one is 'done right'. That's what's tough about a reboot....as my original Braniac storyline was first intended as a possible SR sequel way back when. But now...there's some connecting aspects that can be left out, but it kinda' feels like the first chapter/film needs to be 'gotten out of the way' first...when it really needs to be impactful as possible to reestablish the franchise sequel or no sequel. And I very much feel that a big key to the reboot's success is offering a villain other than just Luthor again....so I dunno. Maybe Metallo, who can also serve to introduce kryptonite into eth storyline...but I generally don't like that character very much. It seems that so many of his really heavy-hitting villains depend on his being well-established, or are more suited to shorter-form/episodic use. It's a tough call for me.
I guess if you use Metallo, you could wait until near the end of the film to reveal that he's robotic and powered by Kryptonite...and then reveal at the end that Luthor was behind it. In the meantime, he could come off as possibly being another superbeing or what have you that makes Superman wonder if there's a connection between the two.