Yeah, I totally agree that duality would be a perfect theme, and I think it's best suited for the third installment. The obvious duality concerned with Batman/Bruce Wayne, Harvey Dent/Two-Face, and perhaps a deeper struggle within both...
...The Nolan/Bale interpretation of Batman, for example, is that of a creature of the night that is meant to strike fear into the darker corners of Gotham City. How must the Batman appear as a hero to the good people of Gotham while still placing fear into the hearts of criminals? Wouldn't his heroics make him seem somewhat "soft" to the crime community? It seems that Batman would have to overcompensate with ruthlessness so not to tarnish his image. After all, Batman is just as much of a hero as he is a vigilante, and yet the two things seem to contradict one another. Seeing as the Gotham public is well aware of the Batman at this point in continuity, it seems like an obvious direction that the character could be taken into during the next two films.
Perhaps they already thought of this? And the reason for calling the film "The Dark Knight" is a hint that Batman will indeed become more dark, more monstrous, and more frightening?