I thought it was a great way to start off a cinematic universe because it allows for Batman to be reborn. Essentially, the story follows Batman as though he is re-experiencing with his childhood trauma through the lens of the aftermath of BZE. So what we get is the same sort of origin story stuff but within the context of an existential crisis. Just like Nolan takes young Bruce up to the point when he would have shot the man who killed his parents only to set a course to becoming Batman, Snyder takes an older Bruce up to the point when he would have killed the man he projected his feelings of powerless onto only to set a course to recommitting to Batman.
Batman sees Superman as the greatest threat to humanity because he is struggling with PTSD. One of the symptoms of the illness is "distorted thoughts about the trauma that lead to assigning blame for the event to themselves or another person." The Martha scene is a happy accident, but PTSD often works with environmental and emotional triggers. "Save Martha" doesn't heal or cure Bruce, but it does snap him out of his flight or fight response. As I discussed last week, The West Wing did a great episode on PTSD called "Noel," and it explicitly suggests that as soon as Josh (the PTSD patient) can identify what is triggering his PTSD responses, he can start the process of getting better. Josh experiences the sound of Christmas music as sirens that blared the night he was shot during an assassination attempt. Working on a crisis involving a pilot who became suicidal after being shot down also affected Josh because the two men shared the same birthday. "Save Martha" and seeing Lois protecting Clark the way Martha Wayne tried to protect her family allowed Bruce to finally see the truth of himself.
For me, it is a satisfying finale because what saves Batman is that he is given a chance to be Superman's hero. He gets to make a difference. He finds his purpose and power again through Superman: his trust and his forgiveness. Superman, by contrast, was beginning to believe that perhaps no one stays good in this world, so Batman's ability to see the light before crossing the line into full darkness is enormously valuable to Clark. Clark spent most of the film defending and believing that the government and the public would ultimately recognize and join him in his cause for hope and justice. He tells Lois that he doesn't care what people say about him, defends the power of the press to a cynical Perry White, and tells Bruce Wayne that the rest of the world doesn't share his negative opinion of Superman. Superman appears before Finch's committee believing that having a conversation will help, and he's so optimistic about the process and humanity that he doesn't look for bombs or threats in his midst. At his lowest point, Superman starts to lose faith, so Batman's ability to see a path back to the light matters.