If anyone's watched JL: A New Frontier, The Centre could easily be replaced by Brainiac mind controlling people all around the world and creating small secret societies in his name.
Would act as a very good origin story for the JL and explaining why people as varied as Wonder Woman and Green Lantern come together.
I liked the JL: Frontier movie but wouldn't want to see it in live action - even if the villain were changed to Brainiac.
If Brainiac is used, I'd like something along the lines of DC Universe Online (minus the exobytes turning civilians into superheroes). Where he comes to collect and digitize all information in the universe then destroy the organic material that it originated from. That story would give an even more valid reason for the heroes to team up since he'd want to get everything from the planet: Themyscira and Atlantis would be included in that.
It could go like this: Brainiac comes to this galaxy in his quest to collect and digitize all of the information in the universe. He has taken Mars long, long ago which explains why life has never been found there (but evidence of past has). He passed over Earth because it was just after the meteor that killed the dinosaurs so there wasn't much substance for him to take. He went elsewhere planning to return when life had reflouroushed on the planet. The band of Martians that escaped the taking of Mars fled to Earth after Brainiac had left it alone in order to carry out their lives in a new home.
After humanity emerged, they mingled with the society to live among them with shapeshifting abilities to look like them. In the present day, J'onn (MM) is the last of the surviving Martian remnant but continues to live among the people of Earth. When Superman is revealed to the world, he is intrigued by how humanity reacted to the fact that he's an alien despite looking like them. He gets in contact with him after the events of MoS just to make his acquaintance. But when Brainiac comes, he is able to accurately identify the level of threat and recounts what happens to Mars.
So after the world goes into panic as Brainiac ships begin "bottling" cities and abducting civilians, the hidden heroes of the world such as Flash and Batman come out into the open to combat the threat. MM and Superman can easily scoop them up into the cause as a united front against the invasion.
And since Brainiac doesn't discriminate against life on the planet, the oceans are a target as well. When bottles start appearing near Atlantis, it attracts the attention of Aquaman. Same happens when Brainiac ships descend on Themyscira (the advanced knowledge of magic throughout the other parts of the universe allow him to see through the cloaking and what not), Wonder Woman goes into action, eventually leaving the island in desperate attempt to find the source of the trouble.
Then the plot can take off from there and you have your heroes united against a threat that isn't so out there that it breaks the tone and feel of Man of Steel (I'm positive that they can design Brainiac's look to make him look on level with Zod and his technology as far as believability). Plus, he can even be tied back to the events on Krypton or even the aftermath - when he learns that a Kryptonian actually survived the destruction of the planet, he is even more attracted since he believed that he failed part of his mission when he lost the contents of Krypton in its destruction.
So yeah, just some ideas thrown out there. Now that I've gotten to thinking about it, I like the idea of using Brainiac even more than Darkseid. For the first movie at least.