Now that "The Dark Knight Returns" has finally been animated in to two films, the next logical choice for Batman is Knightfall. This 90's mega series was DC's Bat answer to the Death of Superman. And like that story it was extremely popular and ran too long.
A single animated film like "Superman/Doomsday" would truncate the story too much losing key elements of the saga. Jamal Igle thinks it should be done as 3 films and is currently running a Facebook thread on that hypothesis. here's how it can be done in 2:
Cold open. Batman fights Biis in the snowcapped mountains and is aided by Azreal. They defeat him but Azreal demonstrates his power and mental instability. He collapses in Batman's arms.
Bane breaks open Arkham Asylum (with Dark Knight Rises Bane is an "A" lister known to the general public and doesn't need a long Vengeance of Bane setup). Batman gets the call in the Batcave and tells Azreal to stay behind. He and Robin got out into the madness of Gotham.
The second act is pure fights. Mad Hatter. Killer Croc, two-Face and finally Joker and Scarecrow. Batman arrives alone to the Batcave and is beaten by Bane. (in a deviation Jean Paul could be in the cave and unable to help. This gives him the motivation for revenge). Bane tosses Bruce's body into the center of town.
The city gets worse. Robin, knowing that the city needs a Batman, convinces Azreal to put on the suit. He's only supposed to show his face but his conditioning leads him right to Bane. This fight is more brutal and ends in Azreal's victory. The hero won but it leaves with an unsettling tone.
It's three months later. Azreal is now an armored batman, working alone. Robin is blocked from the Batcave.
Bruce is slowly healing, relearning martial arts. No magical healing properties, just a slow recovery like in Dark Knight Rises.
Azreal fights Joker. He kills one of Joker's henchmen. (rather than the 'd' lister Abattoir)
Bruce meets Azreal on the rooftops and asks for the return of the mantle (no reason to have two confrontations in the Batcave). Azreal, still with blood on his hands, refuses and batman chases him acrossthe city. We have teh bridge sequence, Azreal losing more and more of his mind to St. Dumas.
We end in the Batcave. Bruce beats Azreal by his wits and his connection to the darkness. There is only one Batman.
This version loses Bane's henchmen, Shondra Kinsloving and even Nightwing but keeps the overall story intact. A good guide for this cleaner version is Denny O'Neil's prose novelization of Knightfall.