Nolan took the Batman franchise to the top of Wayne Towers and beyond. We needed something, anything to cleanse or palletes from the bitter taste that Schumacher left. But will Warner Brothers want to back to Schumacher's comic book feel? Will they want to ride Nolan's (and the other recent superhero franchises) theme of superheros exsisting in our modern day real world? I hope the latter is true.
I have read articles where people are sick of the same villians being reproduced from the 90's Franchise to the Dark Knight Trilogy. But it's funny how everyone likes Ledger's Joker over the iconic Nicholson's take and Hathaway's version of Catwoman over Pfeiffer's. I would argue Seymour Hoffman would do a better job of the Penguin than DeVito's freakish, uncomfortable at times Penguin. Anyone would've done better than Tommy Lee Jone's Two Face so Eckhart didn't have too much to worry about even though his story arc was way too rushed. Carrey's Riddler would've been tough to match but I am sure Johhny Depp would be game.
I do get the arugement of wanting to see Batman fight Killer Croc or Clayface. I do understand how comicbook junkies want to see the supernatural powers of the Lazurus Pit. I argue we can still see that in the Nolan-like universe. In GI-Joe: The Rise of the Cobra,an invisble suit was easily explained as taking pictures of what is behind you and projecting them in front of you. So why not explain a man dresses in a suit that morphs in and out of strange forms? Why not explain a huge man has a rare skin condition or his DNA was mixed up with crocodile DNA to fill in certain DNA gaps? Even Man-Bat's backstory can explain his freakish appearance.
There are plenty of villians the reboot can explore that don't require supernatural powers. Deadshot, Black Mask, Victor Zsasz (Jason Statham anyone?), The Mad Hatter (Daniel Day Lewis), The Ventriloquist, Calendar Man, Harley Quinn (played by Rooney Mera?), Hugo Strange (Robin Williams or Jeff Bridges) and Tweedledee and Tweedledum all don't have the same other world characteristics as Croc and Clayface.
Let's leave all that supernatural stuff to the kiddie Team Jacob girls. Or if Warner Brothers was deadset on supernatural villians they could take a page from the X-Men Series that made mutants believable in the real world. Kinda like MIB makes aliens seem half belivable especially when they disclose Lady Gaga, Dennis Rodman and Joan Rivers are aliens.
Even if 5 years pass before Warner Brothers begins discussions on a reboot, I really can't see them wanting to do a complete 180 from Nolan. Iron Man, Spiderman, and Superman will still be current so I suspect WB will want to stay true with them. If it ain't broke don't fix it. The only think broken about Nolan's Dark Knight Trilogy are box office records.