The more I think about it, the more I'm starting to believe that Justice League may already be a soft reboot for the franchise.
1. Flash has already been confirmed to be able to time travel (BvS scene).
2. All the trailers have showcased the heroes on earth during the invasion (shots with red skies) except for Flash. (maybe he's off in the past?)
3. The marketing now has shifted from batman, to WW now to a lot of Flash stuff.
4. He's the one character that has never "fought" before, and the youngest, making him the underdog of the entire league. This would make even more sense to have him be the one who saves the day.
5. A shot in the trailer where he is running, that's different than other shots in the same vain. In this one he's surrounded by lightning instead of you being able to work out the world around him.
6. That BvS scene was made for a future pay-off.
7. The Batman movie is supposedly a prequel or at least set before BvS. (after flash makes right with the world)
8. A few months ago WB announced that the universe if more loosely connected a la the X-Men franchise instead of a traditional world building and pay-off every "phase" franchise.
9. Wonder Woman 2017 wouldn't be effected by it, as far as continuity goes, since it's mostly set in the early 30s.
10. The "Flashpoint" movie in the works could very well be about Barry getting out of a time loop he's stuck in, and less about time travel.
11. Supes is dead and more than likely comes back as evil, making him an impossible powerhouse for the league, leaving time travel as their only option. This is more than likely where the flash/knightmare scene comes into play.
12. Extensive reshoots