The games are fantastic, they did so much more right than they did wrong. The characterization of Joker, Harley, Penguin, Catwoman, Killer Croc, Scarecrow, ect... are fantastic. Even many brief appearances like Mad Hatter and Zaz were well done. Arkham City's Riddler was one of my favorite parts.
That said, I agree w/ your points. The Ra's story seemed hurried and forced....just kind of a small taste of the comic Ra's. He's a deeper character and, w/ so many other characters competing for screen time, he wasn't really done justice. He dies a lot and comes back. I hope he will one day make a comeback in a sequel and his potential will be explored more.
More could have been done w/ Hush but I felt this was just set-up to a later game so I'm giving it a pass.
Dr. Strange should have done something w/ the Bruce Wayne knowledge other than taunt Batman about his parents death. I understand that he put Batman into Arkham City in the first place b/c of his knowledge but I would have liked to see him raid the mansion or put Alfred in danger or something. I know there is a nice mansion challenge map but I would like to see that in the game.
Bane was simply a brute monster in the first game. I can see that and understand it given his long incarceration and then sudden rush of venom. In the second game though he clearly mentally re-adapted to the venom and so it would have been nice if he had have displayed more cunning.