The Knightmare scenes were supposed to be what JL2 was.
JL2 was supposed to be the Knightmare future. JL3 was Batman sending Flash back in time to undo it, and then it would have been the entire JL plus the newer members like Shazam, Atlantans, Amazonians, etc. Against Darkseid's Armada in an all out war.
I gotcha. That makes more sense, though still seems pretty hard to follow.
Honestly, Batman Vs Superman should have set up the Justice League better, without the Superman/Doomsday storyline. Then Justice League movie would have been the Doomsday storyline that takes up way more than 20 minutes it did in BvS.
Then the next phase after Justice League is Man of Steel sequel, titled "Men of Steel" like the comics where you have several people trying to take over the mantle of Superman. It would culminate with Superman awakening and slowly regaining his powers as he takes on Cyborg superman Hank Henshaw.