Let's start at the beginning:
-At SDCC13, it was announced that Batman would meet Superman on film.
-After SDCC13, we heard that WB was looking for an actor to portray an older, more experienced Batman, then Ben Affleck was cast.
-WB CEO Kevin Tsujihara said that this version of Batman is "tired, weary and seasoned."
With the emphasis being placed on Batman being an experienced veteran, I have come to the conclusion that they are straying away from an origin story. Now, his origin might be referenced to or shown in flashbacks, but the main point is that he's established as crime fighter. So, I've found a few stories that would not need to show the origin for the hero or villains.
*While I think the Joker is overused, he is no doubt the most popular and marketable to the general audience.
**I don't think they're going for sidekicks, so I didn't include Nightwing/Robin or Batgirl.
1. Night of the Owls
My first pic would be the more recent "Night of the Owls." Batman has already been established, and WB can introduce a new villain(s) that haven't been done before. His parents and even potential brother could be referenced as well.
2. Hush
My favorite Batman story, "Hush" would be an excellent movie in my opinion. It has the feel of an action/drama. While it might be difficult to get all of those villains on screen in a 2 hour time frame, some parts can be cut, or it can be a 2-part movie (I kid). I'd pick this because you can establish serious villains without having to set an origin up for each one. It'd also establish Batman's detective skill. However, this might be a better story to close a saga than open it.
3. Arkham Asylum
Similar to "Hush," "Arkham Asylum" also has many well known villains involved who don't require an origin story. The game based on the story holds a Guiness record for "Most Critically Acclaimed Superhero Game Ever," so imagine how awesome a movie about it could be.
4. Knightfall
While already loosely adapted in "Dark Knight Rises," "Knightfall" would be a good way to introduce lesser villains that Bane gets out of jail, and gives us another chance to get a proper Bane. The backbreaking doesn't have to happen, perhaps he just pumells Batman to near death, or severly wounds Alfred. Also, Azrael doesn't have to become Batman, or even be in the film.
5. The Killing Joke
Perhaps the all-time fan-favorite Batman story, "The Killing Joke" would make a dark and twisted movie. Barbara doesn't have to be Batgirl. Her crippling at the hands of Joker would still be as sickening an gut wretching if she's just Gorgon's daughter. Perhaps she becomes Oracle at the end. And again, Batman's most popular villain is in the spotlight, in his sickest potential.