Actually, I love Murphy's Scarecrow, and I was sad to see so little of him in The Dark Knight. I wanted him to be The Joker's supplier of laughter gas, that would have made perfect sense in the Nolan-verse. (Although I'm also a bit relieved that didn't happen.) I'll bet good money that Scarecrow won't be a major player in the next film, he's a spent force now.
There's really no major villain left. Which is why I was convinced The Riddler would be the next one.
-The league of assassins/shadows are a spent force now that Bruce kicked their collective asses. (And Talia al Ghul will not happen)
-Freeze is too silly
-Catwoman can't work on her own
-Ivy is too silly
-Riddler is out
-Penguin is too silly
-The 80s/90s villains are stupid: Black Mask, Bane, Zsasz, KGBeast, etc all stink to high heaven. They're campy without being fun.
-Killer Croc, Man-Bat and Clayface make no sense in the Nolan-verse
-Harley Quinn is too silly
-Dr. Hugo Strange and Doctor Death are too old-school
-The Mad Hatter is one-note and an uninteresting villain
Can anyone tell me who's left? No really minor villains will fit in such a project. I'd love to see Batman fight The Flamingo and the drug trade, but I doubt that will happen as most people have no idea who that is. And let's face it, 90 percent of Batman villains are cheap gimmicks in search of a character. Although I love The Cavalier of Crime, I wouldn't want to watch a film where he's the villain. Or how about The Monarch of Menace? Or The Snowman (the bastard offspring of a human woman and a male yeti)? Or Zebra Man?
I'm afraid Black Mask is one of the few that would make sense. Ugh.
From the situation Gotham City is in, and the possible non-supernatural villains left, my personal preference would actually be Lex Luthor. But that's not gonna happen since he's too mired in Superman lore.