It seems simple to me. Now i would prefer that that without any official statement, the DC Cinematic Universe is already being established with the Nolan films. George Lucas did it with Star Wars.
There is already the modern legend of the Batman. Judging on the rumors, and the footage so far of the MoS, Clark has had a hard time figuring out who he is and where his place is in the world. Now take into consideration they government did not accept Batman for a long while and from the MoS comic con footage, they ain't warming up too Superman too well (which is just realistically how it would be in our world).
I'm gonna presume Zod is gonna leave his mark on the world in MoS. That being, they will fear Superman and look at Superman and his race as major threats to the world. If anything alien happens again to the world, you know who's gonna be blamed first.
Around the 1960's era, there were many sightings of Alien sightings and UFO sightings in America. With that being said, one of them are definitely true, that being the Earth had picked up a new settler, the Martian. During this time and modern times, the Martian has been learning about the human race and adapting to its culture.
The Earth is attacked by an Unknown beings from the stars. This causes a major global threat, and attacks all over the world are shown. Superman is the first suspect of the government. Meanwhile, Bruce Wayne can come out of retirement, when the worlds new hero is leading suspect. That would cause Bruce to go back into detective mode to try aid the earths current hero, and it would also lead Bruce to looking at previous alien sightings, especially most recent ones *cough* the 60's.
At this time doom, even the more ancient part of the world has been attacked. One being the hidden ancient amazon's. These amazons were tough warlike warrior woman that surfaced during the days of the Olympians and ancient Greece who settled on a island which is hidden by ancient technology, not understood by the modern man. And the underworld city of myth, Atlantis, which for thousands of years, has survived hidden deep in the ocean. Atlantis would consist of a race on ancient beings known as atlanteans, which pre date homo-sapiens even though they resemble homo-sapians a fair amount. These ancient parts of the world would surface their champions, King Orin of Atlantis and Princess Diana of the Themiscrya to investigate the cause and stop the culprit of them global attack.
At this point there would be a reason for Aquaman & Wonder Woman to have surfaced into mans world and they are obviously gonna want to speak the worlds champion, Kal-El, who the goverment also believe is prime suspect at the moment to the attack.
During this time Batman could peace the peaces together with the Martian and seek out Superman, who also at this time is being sought out by Orin & Diana. And Superman will be on his way to oppose the threat, who has got Superman's attention.
Then the world would have to see this Dark Lord of an unknown world from the stars defeat the man of steel. Then the stakes would have risen, and it's gonna take more than Metropolis' champion to save the world this time.
A nice little philosophical opening line from Bruce/Batman (Played by Bale!!!!!) would be Epic.
Thats also just my rough idea. I definitely think they should go "What would this be like if it was real?" tone like the Dark Knight trilogy. WB shouldn't be trying to watch what the Avengers done. This has the potential to be so much more.
YES!!! 
