I like the Michael Emerson as the Riddler idea. My own choice has been David Hyde-Pierce from Frasier. In Dark Victory, the Riddler is drawn to look very like him. But Emerson would be a fairly similar choice - smug, smart and creepy.
I'd prefer to see Paul Giammatti or Toby Jones for the Penguin, but wouldn't complain if Hoffman was cast.
I agree with Norrin Radd's comments that the actors for whatever characters are in the next movie will be unexpected. No-one saw Ledger coming or Cillian Murphy for Scarecrow. In a year, we'll all be marvelling that Nolan has cast two apparently strange choices for the movie - in another 2 years, we'll be marvelling at how good they are, while swearing that we knew they'd be great all along.