It would still be an invasion movie though. Not doing a full on invasion in the first film isn't a bad idea, but I wouldn't scale down so much as to use Atlanteans as villains.
The JL Mortal film had a decent idea in using Maxwell Lord and OMACs as villains. I think Maxwell Lord (or you could swap him with Vandal Savage, and reveal his powers at the end in an epic battle), OMACs, Checkmate, and Amanda Waller would be formidable villains, maybe save them for a second film though, like you said based on Doom/Babel.
There are a decent amount of ways you can go for the first film. It wouldn't be a bad idea to save a Darkseid invasion for the third film, after they've set up the New Gods and foreshadowed Darkseid's invasion throughout the cinematic universe...
Maxwell Lord, Amanda Waller, OMACs, Vandal Savage, Amazo, White Martians, Injustice League, Darkseid, Brainiac, Doomsday, Despero, Mongul, Starro, Crime Syndicate, Doctor Destiny