Personally, I would love this as a Mr. Freeze/Penguin film.
With the first, we had the "mind game" villain via Riddler, which was perfect for a young, mentally unbalanced Batman still finding himself and his inner hero. But with Gotham flooded and infrastructurally brought to its knees, we now need the powerful, elemental force kind of foe to really test Batman as a hero, and Freeze would be perfect. Meanwhile Penguin can also fully level up as the king of crime/mob activity in Gotham and be the guy pulling strings everywhere in this new fallen Gotham. Keep Joker in jail in this new Hannibal Lector kind of role that the deleted scene showed and that would be great.