I'm at a bit of a loss for who would make the ideal villain for this. Darkseid strikes me as a bit too similar to Thanos. Starro is pretty silly, but you could do an Invasion of the Bodysnatchers type thing with him. I suppose a loose adaptation of Morrison's JLA arc with the white martians could have a lot of potential, and it's got a pretty solid core. Supercreatures come to Earth offering to fix all of humanity's problems, but it's too good to be true. Whatever they do, I think making GL and Flash the centerpiece would be the right way to go. By then, the audience will already be well familiar with Batman, Superman, and Wonder Woman. Make Flash the counterpoint to them, as the young superhero who's actually loved by his community and John Stewart as the military man sent to keep tabs on the rogue superhumans. Use the two as perspective characters for the audience and make the blossoming friendship between the two the heart of the story.