Honestly, it wouldn't matter, and it wouldn't even have to be a movie adaptation of a comic book Crisis story. That would be very hard, and likely tough on the viewer.
But all Crisis stories have some similarities.
Picture this--the Justice League is doing its thing, and suddenly finds themselves confronted by a bad guy bent on destroying the world, not just to rule, but to reshape in his own image. Think Zero Hour.
Given that Hal Jordan is not even in the DCEU yet, I would NOT make the villain Hal Jordan. He would be a villain we haven't seen. Time travel would be important to this crisis, but I want someone even more powerful than that. He can rewrite the whole universe in his own image.
The reason I want this villain to have this kind of power is because of the end game, which is of course he is stopped by the Justice League, in such a way that the entire DCEU is reset.
Good will win, but it's not a slam dunk 100 percent victory. The end result would be the DC universe that is more in tune with what made these characters popular in the first place. I don't want just time travel involved because I don't want the reshaping of the DC Universe to be limited to just Earth. I want Krypton affected. I want the Guardians affected.
History will be changed and continuity will be thrown out the window. The next time we see our characters, they will be part of this new continuity, be it in their own movie or in a Justice League one.
It's not the only way to reset the DCEU--but I really think it needs to be done, and one strength of the DC universe is that there is so much precedent.
Hell, you could simply do a story where we establish the multiverse. The Earth we have been following can be called Earth 23. The heroes from Earth 1 come to Earth 23 for help. The heroes of Earth 1, all have counterparts to Earth 23. Some of them are played by different actors, assuming you want to recast (cough::newyoungerBatman::cough). They have their adventure and win the day. Hell, you can even kill off some characters. It won't matter because the Earth 1 heroes are the ones we will follow from here on out.