I'd like to see Harley Quinn played by Gigi Edgely (Chiana from Farscape) as maybe a Joker stand in basically. They could keep her origin nearly intact from Mad Love - although I do think that she and Poison Ivy could be an interesting duo. With Ivy being an environmentalist/Al Gore worshipping/hybrid pushing hippie chick who sees all the crime, corruption and violence in Gotham as hurting the environment. Teaming up with Harley partially because she's studied Joker extensively in prison and basically sees her methods of violence a means to an end.
Penquin is an almost must have - I like the above idea of keeping a sort of Burton-esque Penquin - but keeping the more B:TAS form of him, as basically an eccentric bird lover, who happens to have a taste for wearing tuxedos and shaped like a penquin. But I'd keep him a tad more unhinged in private - not quite as OTT as DeVito's but twisted. Maybe instead of being hideously deformed - he's just a rather short man with a rather long beaklike nose and webbed fingers that resemble flippers when he wears gloves. Information broker, Casablanca type does fit the character.
Killer Croc - he'd be interesting, Batman hasn't really gone up against a really TOUGH character in the Nolan-verse yet. Someone that towers over him and can basically kick his ass from here to Metropolis.
Catwoman - I think she works best as a sort of anti-hero/Robin Hood type character than an out and out villaness. I'd ditch the prostitute angle though. Although, I think I could see her as being a sort of well heeled girl from a good family, who's family was killed during earlier mob wars and basically took everything they had, from businesses to property to baubles. Possibly even went away to underake a career as an Olympic gymnast - which could help explain how she can move the way she does. Works as a cat burgler stealing from the mob bosses and criminals that stole from her family and giving part of her 'take' to charities. Sets herself up as a 'do gooder' as Selina Kyle, attracts the attention of Bruce Wayne, but only because she's going to rob Wayne Industries because they bought up one of her family's companies. Bruce and Selina meet up in their alter egos and fight briefly, the masks come off and basically she becomes Catwoman as more of a persona than just a nickname.
Plus it lets someone else fight Harley Quinn or Poison Ivy without having Batman hit girls LOL