Alright, so I think I've cracked the knightmare/flash scene. It's a future where Bats and Supes aren't working together, and DS has taken advantage of that. All the JLers are scattered, with nobody working together. Possibly, nobody trusted each other, so nobody helps each other out. Basically, DS has divided and conquered. Nobody has united, so they have all fallen.
The scene with Bats/Supes shows that as a result of this disunity, Lois has died, at some point. Obviously, Supes and Bats having never becoming friends, Bats has no idea what her death would mean to Supes. So he's let her die, probably because he chose not to save her because she stood for helping the alien, and he thus didn't care about her. Without that Martha moment, Bruce sunk into darker depths and likely only cares about killing Supes and Darkseid rather than saving anyone.
Flash's warning is him come from the future to tell Bats that "Lois is the key" to understanding Supes. He says that Bruce "was right about" there being a 1% chance Supes could be our enemy and we should "fear him" if something happens to Lois, cause she is the key to him snapping.
But why warn Bruce about a danger he already knows? That was my problem with the whole scene until I realized: the JL is the prevention of Injustice style Supes.
Flash, knowing that Supes is to be feared, has come back to tell Bruce that he needs to "find them" (the JL members) so that they can work with Supes and keep him good, and Lois safe. But the message is "too soon" and Bruce doesn't understand it.
But after the Martha moment, and seeing Lois come to Supes' aid, and possibly the way he acts with her before he dies, Bruce understands the message. He knows that he should have understood that the key to keeping a good guy good is understanding, empathy, rather than confrontation. He was right to worry about the 1% chance, but wrong to launch a preemptive strike. Instead, he should have talked and worked to get to know Supes, because knowing what makes him tick is the way to prevent the 1% while still taking advantage of all the good Supes could do.
Finding the other metas is the way to make sure none of the other metas become dangers...which is the most effective measure for preventing more disasters. Bruce sees that clearly after learning about the other metas and working with Supes/WW to destroy DD. So even though Supes is dead, Bats ois gonna find them, not because he fears Supes anymore, but because it's the thing that will be his real legacy; it will be the most important thing he ever does, not killing Supes (which is what he earlier thought would be his biggest contribution to protecting the world).
So when Bruce says he "failed him in life" (a statement I thought was strange, given he saved Martha) he is talking about that previous future, where he let Supes down by not being his friend and letting Lois die.
But now, he won't fail him in death, cause he's gonna change his ways, and become trusting....so that his lack of trust doesn't lead to the dystopian future he saw and was warned about. Once he does that, Flash's warning has been heeded, and the future set right.
