If WB/DC want to get Darkseid on the big screen without the general audience thinking it's a copy of Marvel (I know it's the other way around, but non-readers don't know that), then they almost have to use him in JL. And really, Johns' first arc was more or less a movie script anyway. A few tweaks & it would work.
As for topping him in JL 2, I say go for the Crime Syndicate. After fighting the evil outside the gates in JL 1, it makes perfect sense to fight the evil "within". Or, in this case, exact mirror images. I'd change it up so that Superwoman is an evil WW instead of Lois Lane, and Owlman is Bruce & not Thomas Jr. Sort of like in "Justice Lords". And you have the actors play dual parts.
I'd save Brainiac for a Superman solo.
I'd tie it all in with hints in the solo movies forshadowing the Syndicate coming in JL 2, and then the solo's in "phase 3" would foreshadow Darkseid's return for an adaptation of Final Crisis in JL 3.
They've said 9 films after JL, right? to hell with Sandman & others, I'd love to see something similar to this:
Man of Steel: complete
Man of Steel 2 (Bats vs Supes): on the way
Justice League: Darkseid invades. Adapt JL: Origin by Johns.
Justice League Confidential: Wonder Woman. This would be where we would see, in flashback, her time on Paradise Island. I'd go full on "Clash of the Titans" with it. Mythological creatures, Hades, Zeuss, you name it. Show her as a badass warrior. Guest-starring Bruce Wayne at some point, helping her set up a civilian I.D.
Man of Steel 3: Doomsday crashlands on Earth, and Superman with no idea who sent him. Guest-star Wonder Woman. Superman dies at the midpoint. Funeral happens, mourning period. End on a Cliffhanger: Superman appears, suddenly alive (but it's actually Ultraman in a Superman suit. Some people hail him as the "second coming".
Justice League Confidential: The Flash. Guest-starring Green Lantern (Hal or Jon, no difference here) and Cyborg. A CSI drama with superheroes. News reports on "Superman activities".
Batman. Guest star Wonder Woman & "Superman". WW has doubts about "Superman", Batman investigates while also dealing with Gotham. Ends with "Superman" revealed as Ultraman & the arrival of the Crime Syndicate.
Justice League 2. Batman, WW, Flash, Cyborg & Green Lantern vs the Syndicate. When all seems lost, Superman returns to save the day. His resurrection made possible by the codex hidden in his cells. Jor El's final gift.
Justice League Confidential: Wonder Woman 2. While still adapting to "mans world", Paradise Island is attacked by Circe & the Female Furies from Apokolips.
Batman 2: Batman does Batmanny stuff. Investigates the Dark Side Club in Gotham City. Perhaps a gang war between the Dark Side Club & Penguins Iceberg Lounge.
Justice League Confidential: Guardians of Oa. The Green Lantern Corps, led by Hal & Jon, vs Sinestro. Guest-starring Superman in a cameo. The universe is at war: Apokolips & New Genesis have fallen, and everyone wants a piece of control. You could really throw in the cosmic characters here. Lobo, Thanagar, Mongul, etc. The Guardians warn that this is only the beginning.
Justice League Confidential: Injustice League. A villain-centric film. Luthor amasses the Injustice League. Every villain you can toss in there, with adequate screen time for the big players. Could intro Black Adam. They fight each other at first, naturally, with Luthor striking a bargain and forming a league. Libra appears.
Justice League 3: Final Crisis adaptation. No monitors, no Mandrak. Time begins to break down. Injustice League is forced to side with Libra. Cyborg is destroyed, instead of killing Martian Manhunter. Batman captured. Granny goes to Oa. Superman taken by a mysterious figure to the future (instead of by a monitor into the bleed) to see a machine that can save the timestream. Since Michael Irons is a badass, let it be Alfred that Darkseid incarnates into. batman shoots DS, Batman is killed (for real). Superman returns from the future to battle Darkseid. At the end, he makes his wish, Earth is saved. In the epqilogue, we find out the strange hooded man from the future was Superman himself, older.
Justice League Confidential: Crisis Aftermath. The World rebuilds. The heroes mourn Batman and Cyborg. Wonder Woman contemplates her mission, now that the God of Evil is destroyed. Clark Kent asks Lois to marry him. Nightwing becomes the new Batman. Wonder Woman returns to Paradise Island. The Amazons fade from our plane, ala Infinite Crisis, taking WW with it. Flash fights some rogues. GL returns to Oa.
Man of Steel 4. Lois & Clark marry. Brainiac arrives. It's revealed that Brainiac was the one who sent Doomsday to kill the Kryptonian. Your general Superman vs Brainiac story. At the end, Superman narrates as we see the world, through montage, turn into a futuristic utopia. During the montage, we see Superman build the machine that he will later show his younger self. Here we'd get the ending of Millar's (or was it Waid?) planned story...as the sun goes red, and the Earth slowly dies, we see that Superman is the last being on this barren rock. His powers almost gone. He looks to the sun, smiling, as he says "It's been a good life. To be continued..." As the sun goes nova, the Earth & Superman are destroyed, their remains & atoms spread across the stars. An after credits scene reveals that millenia later, a piece of Kal's skull survived, and passes through a wormhole, and lands on ancient Krypton....
Ok, that would be 12 after JL. But I'd still love to see something like that.