I know a risky but possibly quite doable solution: follow the cartoon.
Set up a war between Apocalypse and Brainiac. Make it clear that Superman has a history with both Darkseid and Brainiac. Then follow the plot of the Justice League episode 'Twilight (of the gods)'.
MOS 2 introduces and focuses on Lex Luthor, Cadmus, and Brainiac. Then JL 2 follows the combined stories of the JLU arc from 'Flashpoint', 'Panic in the Sky', and 'Divided We Fall'. MOS 3 could have Luthor come back angry as ever and obsessed with reconstituting Brainiac to become a god.
JL 3 goes in with a condensed adaptation of the story from 'Alive' then the last 2/3 of the movie is a fleshed out plot based on 'Destroyer' which would NOT be teased in the trailers to make Darkseid's return have maximum "holy ****" impact on the audience.
In my mind, that'd reconcile them using Darkseid in the first movie if they follow that plan. The story arc you see through the episodes I mentioned gave me my love for JLU and why it remains one of my favorite cartoon series of all time. Granted it'd be super tricky to adapt without making the thing seem too silly or cartoonish, but with the right oversight, it could blow the Avengers trilogy right out of the ocean.
Update: Here are the links to the episodes in order. I couldn't do it before because I was using my phone :S
Justice League 1 - Pretty much straightforward adaptation of this story
'Twilight (of the gods)'
Justice League 2 - Rewritten to exclude subplots like Question & Superman killing Luthor in an alternate dimension and amalgamating the following
Really only the second half of this episode. Maybe after 10:27 and onwards. Followed up by
'Panic in the Sky'
'Divided We Fall'
Justice League 3 - These but with smaller JL and Legion of Doom rosters (obviously)