I doubt we would ever get a Justice League trilogy- unless they cast young and ONLY make Justice League films in their own continuity- NO SOLO efforts. That would suck.
I think we'll get about one solo film for some of the characters (Wonder Woman, Green Arrow, Flash, and Green Lantern) two solo films for Superman and the three for Batman. The sequels (Batman 4, Superman 3, WonderWoman 2, Flash 2, Green Arrow 2, and Green Lantern 2) would all be in the form of the ONE Justice League film. You could have the threat be hinted at in some of the solo films. And--I'd like to see Superman: Man Of Steel end with the need for a Justice League- so Justice League acts as a DIRECT sequel to Superman: Man of Steel.
Maybe have Brainiac as the main villain throughout the film- then at the films end Darkseid is revealed to have been involved and Superman is killed in a battle. This leaves the Earth without it's greatest hero at the time when it needs him most. Darkseid begins his reign on Earth and Brainiac has left the technology of Earth in ruins.
The Justice League film picks up from here, with the worlds heroes coming together to Metropolis to try and do what Superman could not. In the film- Superman is discovered to be alive and at the fortress and takes off from there.
-R