I wouldn't lump The Ventriloquist in with those guys as being unrealistic. Having a crazy mob boss who talks through his puppet isn't supernatural. We got a sense of how the gangs are now following super-villan types in BB and TDK, with the Scarecrow and the Joker. If a crazy eccentric type gets the job done the crooks will follow him even if he has a puppet on his knee. In fact I'd much prefer to see the Ventriloquist than just another mob boss in the 3rd movie.
I wouldn't mind someone like Killer Croc either, just have a big guy with a skin condition with filed teeth. That's the way he was portrayed in the early comics evne though he just looked like a big lizard.
I wouldn't mind seeing Bale's Batman going up against super-situations, but I understand what Nolan is doing and it's probably best for him to stick to a non-supernatural/powered enivironment. But, if they can push something like the machine at the end of BB, they can push other technology coming into being. Don't know if sci-fi tech could go as far as having a 'plausible' MrFreeze, but maybe it could be worked in somehow.
Thing is, maybe they could work in sci-fi advances, if the characters are as surprised by it's existence as we would be if it occured in our world. Man-Bat might be a stretch too far, but I'd love to see him onscreen against Bale's Batman. edit: As long as he was the tragic scientist type who was trying to copy Batman like in the comics, not just an unthinking monster like in BTAS.