Yeah, that's my idea. I think Croc could be in play if approached properly. Deebo fits the look already, they can just give him some deformities (scale like skin on his back and neck, scarring, tattoos) to flesh out his look, then take more of a street tough angle on him than a mutate. Have him organizing street gangs and making them more dangerous. The character Lister played in Dark Knight appeared to have some influence over the inmates (the Ferry scenes), but it was never stated who he was, seemingly some unnamed inmate, so it would be a nice teaser for him to be Croc and have a bigger role in the next film. It also depends on how many more films Nolan intends to do. Ra's, Two-Face, Scarecrow, and Joker were already used. Riddler, Penguin, Catwoman, Bane, Croc, Talia, and Poison Ivy are the big rogue players left on the table, and you don't want to put too many characters into one film. I think having the Riddler doing more cerebral/cyber crimes and pairing his actions with a more direct physical antagonist (Bane or Croc), thus having Batman tested both mentally and physically, would be the way to go. Dark Knight tested his morality, the next film could test his intellect and physicality. Having him go hand to hand with Bane or Croc in drawn out scenes would be dope.
I just thought the reason he had influence was he was some famous gangbanger/murderer who was the baddest motherfvcker on the whole boat. I'm not sure if I can see him in an organizational role, it was clear from his brief appearance that he has some philosophical and moral insight (or he really didn't want to go back to prison and he hoped the ship would blow up) when compared to the prison guards and the inmates. If anyone is going to fill the "unite the gangs of Gotham" route make it Black Mask. After Riddler Black Mask is the best pick IMO for a primary antagonist.
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“Where the longleaf pines are whispering
to him who loved them so.
Where the faint murmurs now dwindling
echo o’er tide and shore."
-A Grave Epitaph in Santa Rosa County, Florida; I wish I could remember the man's name.