I do believe we'll get a more modern villain with the first Affleck solo film with perhaps a classic one thrown in as a secondary. Something like Hush driving the main story but with the Penguin as a character that also propels the action.
My personal hope would be if they went really
fresh and adapted the Court of Owls storyline. It's a story concerning Bruce's overconfidence when it comes to Gotham which would be perfect for this older, more experienced Batman. It's not too fantastical which I'm sure Warner Brothers is looking for, and it has plenty of action but with psychedelic imagery and a great physical presence with the Court's assassin, Talon. It's emotionally satisfying and something only the comic audience is familiar with, so the reboot will really be starting out fresh.
I don't think it's terribly likely they'll go for it, but it would be perfect.