I'd like to see the Penguin introduced the way he's being used in the comics now... as a kind of mob boss who fronts a high toned club for 'bad boys' called the Ice Berg Lounge.
Killer Croc wasn't always a lizard. Originally he was a wrestler with a freakish skin condition that made him look scaley. He had his teeth ground to points. This character would definitely work in a Nolan film .. just not as a main villain.
The Ventriloquist - now this is an interesting character. Not only could it be done realistically - it already has. See the movie 'Magic' starring Anthony Hopkins. He might even work as a major villain. All it needs are the right subplots and a good script.
Man Bat - now, as fantastic as this character seems, I think Nolan could pull it off. Let's keep in mind that Nolan's Batworld is not realistism but Hyper-realism. That means the characters act like real people, the landscape is presented realistically, and the motivations are realistic ... BUT... there have been fantastic things in both films... the first being the plot involving the microwave device and the hallucingen. We all know that wasn't realistic but we bought it because of the way it was presented.
But, over-riding it all is that we have a guy in an armoured Bat-suit.
So, could Man-Bat be done in Nolan's world? I say yes. Of course, Nolan would have to make some changes to the character just as he did The Joker. Maybe there would be no flight ability. I don't know. But I have every confidence that Nolan could take most of Batman's rogues gallery and make them work in his world.