Clayface wouldn't likely happen. Nolan has made it explicitly clear that he is not a fan of CG. Clayface, while awesome in the cartoon, was also always a villain who kind of pulled Batman out of the reality of it. Nolan's made mention that his favorite thing about Batman is that he's pretty grounded in reality. I figure they'll be avoiding the superpowered villains like Clayface, Man-Bat and the like.
Hush would be workable, but I doubt we'll see that one in action. It was a pretty complicated storyline and it really wasn't all that good to begin with.
If they do a third movie, I'd expect someone more along the lines of maybe Catwoman, the Riddler or maybe even the Mad Hatter. Even Bane would be a possibility (And an interesting one, at that). Judging by the dark tone of the series and the more realistic portrayals, I think Mad Hatter can be effectively written off, as he's rather goofy. Riddler's a possibility, as he's easier to write with less camp. I expect we'll see a Frank Miller style Catwoman in the third installment (A prostitute who gets a kick out of Batman and decides to resort to theft).
Unfortunately, as good as Nolan's been, his style and vision is pretty limiting when it comes to Batman's rogues gallery. If he continues to refuse to stray from his mafioso, grim and gritty M.O., then he's going to run out of possibilities really quick unless he majorly reworks some villains. Let's run through the Batman rogues:
Scarecrow, Ra's, Joker and Two Face will have been covered by the end of this one.
Poison Ivy, outside of her plant schtick, would be effectively pointless. The only other role she serves is as a seductress, which Catwoman covers better. Not likely.
Bane is VERY easily reworkable to suit Nolan's purposes. Let's ignore the Bane that showed up in Batman & Robin, shall we? They fucked him up but good. The real Bane was one of the smartest and most intimidating villains Batman ever faced. He organized a massive breakout of Arkham in order to wear Batman down. Once Bats was at the end of his rope, Bane broke into Wayne Manor, beat the piss out of Alfred then savagely beat Batman and broke his back. Sure, he was super strong, but run an angle of him just being a heavily trained mercenary with crime lord ambitions and you're golden. Very feasible.
Mr. Freeze, like Poison Ivy, doesn't really work outside his schtick. This is tragic, considering the BTAS Freeze was incredibly well done.
The Penguin is doable. Lose Burton's circus act crap and turn him into the affluent, high society criminal he was in the cartoon and comics and he writes himself. Get a relative unknown in there and he could be gold.
Clayface I've covered. Too much CGI, too unrealistic to suit Nolan's vision.
Killer Croc is a two dimensional bruiser. He'd be fun in a one off role of just being a nickname for a generic mob enforcer, but otherwise of no use.
Scarface is realistic and very intriguing, but I'd be concerned about the audience taking him seriously. If they got him just right, he could be perfect, but otherwise risky. If they set him up right at the beginning to do something particularly heinous, Scarface and the Ventriloquist could make for an excellent tragic story.
Riddler could be made to be more menacing, but it's an uphill battle. If they portrayed him as an obsessive compulsive, it could work out really well.
Most anyone else is either too obscure (Lady Shiva), too generic (Black Mask) or too similar to/derivative of another villain (Harley Quinn) to be workable.
Running through the list, Catwoman, Riddler, Scarface and Bane would be the best and most likely candidates with little tooling necessary.