From what I've seen from Rocksteady so far in the Arkham series, they really excel in creating these grimy, gritty worlds that can be, at times, horrifying. That's why I think John Constantine is the story they could really tell. Superman is too squeaky clean. Same for Green Lantern and Wonder Woman.
When I say JC, I imagine Gotham City invaded with those fear toxin ghouls (from beginning of the game) at every corner. With villains bordering on the demonic, with jump scares like Man Bat and a terrifying premise that builds tension. Like Rocksteady's very own L.A. Noire mixed with the occult and supernatural crimes that the series is known for.
Granted, the character lends himself to some pretty adult themes and some super powers that just don't translate well into a video game, i.e. demonic summoning, divination, necromancy, and mind control. However, it'd be something I'd be more than willing to add to my library.
Second choice: Jonah Hex. Imagine Rocksteady's interpretation of Red Dead, or the Oddworld games?
I'm sure wherever the studio lands, its production will be top notch. Can't wait to enjoy more add-on content for Arkham Knight. Bring on the Court of the Owls!!