Considering it's freaking Batman, I wouldn't be surprised if Rocksteady worked on another game for him but who knows. Just because Joker is "dead" doesn't mean there can't be another Batman game. I mean jeez look at all the villians you can still work with, there's plenty of possibilities. Not every Batman related thing has to have Joker in it just because he's the most popular villian. I know they can do this because look at how awesome they made Hugo Strange....a villian that's barely been given any attention in the past.
You do make a good point Batman's rogue gallery is huge, they could go in a number of directions, they could go with like black mask or the red hood. Actually with the right writing they could make a great game about a little known villain. Like you said with what they did with Hugo Strange. Especially since these games are geared toward true batman fans anyway.
The plot twists near the end of the game weren't executed properly. I was suspicious of an impostor Joker since Batman was gassed early in the story. I mean, didn't you see that Joker looked healthy then? What was with all this blatant hinting? I'm not oblivious so I couldn't really enjoy Arkham City fully. I seen Clayface Joker coming from a mile away.