I want him back for the next game too, but I'm glad they left him out of Arkham City. As much as I loved the Scarecrow sequences in AA, AC would just be a repeat of that. I'm glad they're potentially making it so Scarecrow is taking time away in hiding to come up with something new and more dangerous.
Check out the easter egg on the boat in Arkham City if you haven't already, the one in the waters before the industrial district (on the boat get out your cryptograhpic sequencer, password CITYOF TERROR, its a very hard combination to hit). Inside the boat is a dead, human test subject, lots of jars containing cockroaches, and a manifest that details Jonathan Crane's request for animal test subjects.
That's as much you can dig up at this point regarding Scarecrow and the next game.
Also near the end, during the bit where Hugo Strange is bombing the place. On a rooftop of a building across from Maxie Zues' club, you can see two bodies in detective mode. They wear the basic red-orange Arkham inmate jumpsuit, but they are also wearing very crude designs of Scarecrow masks. This suggests Scarecrow has henchmen operating, probably brainwashed. This is the only time you'll see any inmate wearing this.
Other stuff is probably still yet to be discovered, but Arkham City is the kind of game that has loads of easter eggs and sequel clues if you look hard enough.
EDIT
Just adding on in regards to the prospect of other characters returning... Pretty much anyone who isn't dead is a possibility. Hell thsi is the superhero genre so (even though they don't often do this in Batman) even someone dead can be brought back by some bullshit, but most likely not. So I guess you can only rule out Joker, Talia and Strange. I'd say Ra's Al Ghul would just be resurrected if he is to return.