As fans, we like for things to have a certain order and consistency to them, which is why we try to justify crazy stuff like The Dark Knight and Batman v Superman being part of the same timeline.
Unfortunately, DC Cinematic Universe producer Charles Roven broke some hearts in an interview with ComingSoon, denying a popular theory that Ben Affleck's Dark Knight from Batman v Superman: Dawn of Justice is the same as Christian Bale's Batman from Christopher Nolan's The Dark Knight Trilogy:
"We really wanted to make a clear demarcation line. Chris [Nolan], Emma [Thomas] and I would talk about how, in his 'Dark Knight' trilogy universe, there are no superheroes. Batman is not a superhero. He doesn’t have super powers. Chris would always say, 'His super power is that he’s a billionaire. He’s got all this money.' I viewed it that Bruce Wayne was a man who took his human abilities, whether they were physical or mental, and pushed them to the absolute peak of the human condition. But he still wasn’t a superhero. Then the villains, whether it was Ra’s al Ghul or the Joker or Bane, they were also all human. They might be aberrant, messed up and diabolical, but they were human beings. When we started doing 'Man of Steel,' Chris and Emma were producers on that one as well. They knew that they were opening up a whole different universe. Even though the fans sometimes talked about, 'Maybe Joe [Gordon-Levitt] is going to be the Batman in ‘Batman versus Superman,'' we knew that was never going to be the case because it is a different universe. In the universe we created with 'Man of Steel,' there are superheroes. There are aliens. There are metahumans. The character of Batman isn’t Christian Bale ten years later. He’s different. He’s come up a different way. His parents, even though they died outside a movie theater, didn’t die outside an Opera theater. We thought about those things. I was involved with both movies and 'Dark Knight Rises' was three or four years from the time I started working on 'Batman v Superman.' It made me feel better that I could go, 'That was that and this is this.' It’s just going to a different place with the material and expanding it out.
So there you have it; a fun idea in theory but just that: a theory.