Here's one potential plan:
Movie 1
Superman is an established superhero who has been squaring off against a series of minor supervillains who seem to be working in a coordinated manner. As the plot unfolds we discover that Lex Luthor is behind the supervillains, using them to probe Superman's weaknesses as Luthor is deeply suspicious of this super-powered alien and wants to pinpoint how to defeat him. When Brainiac arrives on the scene Luthor seizes the opportunity to learn about Superman's alien origins and find out how to defeat him.
Pre-credits action sequence: Superman foils a heist perpetrated by Silver Banshee and and Riot.
Major villains: Brainiac and Lex Luthor (in his corporate LexCorp iteration).
Movie 2
Pre-credits action sequence: Superman versus Toyman.
Main plot: Lex Luthor continues to investigate the Kryptonian technology that ended up in his possession after the Brainiac imbroglio of the first film. Luthor inadvertently unleashes Zod and his gang of marauders from the Phantom Zone. In a twist, Superman and Luthor join forces to defeat Zod and his gang, but Luthor has a back-up plan he's formulating, namely Metallo, whom he intends to use to kill both Superman and Zod.
Main villains: Lex Luthor and Zod.
Luthor's third act henchman: Metallo.
Movie 3
Pre-credits action sequence: Superman versus Livewire and Atomic Skull.
Main plot: The minions of Darkseid infiltrate into positions of power and influence on Earth, setting the stage for an invasion. Lois and Clark uncover this plot and discover the existence of Apokolips and New Genesis.
Main villain: Darkseid.
Darkseid's minions: Kalibak, Steppenwolf, Kanto, Granny Goodness, Lashina and the Female Furies, Amazing Grace, etc.