dent, two face, whatever you want to call him, is dead in this series. i can't believe this is still being debated. i'm sure the character will turn up in another series, but here he's flat out dead.
they are creating new story lines here. the dark knight does reference material in the long halloween, but it is not the long halloween. it has nothing at all to do with it. dark victory has no bearing whatsoever on batman 3, but they could take inspiration from it.
for example, heres my own batman 3 plot:
centre batman 3 around a killer mystery, ala the long halloween and dark victory. A killer is taking out different bad cops, leaving pinned riddles and clues on them. the thing is, the clues and riddles are written on harvey dent's old case files about the mob. it is mighty bizarre for somebody appearing to be two face doing these crimes.
in reality, the whole things just a mind game set up by the riddler, but it takes the film a long time to get to that revelation. it is keeping alive the character of dent in a way, so this plot line has the lasting effect it should.
with that going on, then loosely take dark victory, which is a murder mystery set in the context of gotham's gang wars, but don't make it as clean cut as that. make it messy - lots of little gangs fighting each other.
the villains need to get crazier than they've been in this post-joker gotham, both in actions and appearance. get more costumed foes here, and have a basic freaks vs. mob conflict going on ala dark victory, where the standard criminal element attempts to recover their grounds from the costumed crazies and ultimately fails to do so.
regardless of what may have had been in store with the joker for batman 3, i think the way the dark knight ended was perfect. the joker is caught (for now) but he is destined to battle batman forever. the joker has inspired people similar to him to come out of the woodwork and go to war. note: theyll need an army to be essentially how chaotic the joker is just by himself, who is locked away in arkham asylum.
in the finale of the dark knight, batman is on the run from the police for taking the blame for dents crimes to uphold his memory as gothams redeemer. remember maroni said to batman that the criminals now know that he has no rules, and the joker has none? well, with batman taking the responsibility for these murders, people will think that he now has no rules. consequently, they will dread him even more. it is a kind of un-intended result that can work in batmans favour, giving him street credibility, so to speak.
the freaks/mob conflict has to be so out of control that the police are then forced to come back to batman to help sort out this chaotic mess. this doesnt mean Batman is on good terms with the police, either.