It's gonna be unpopular, but I think Wonder Woman was what went wrong.
Don't get me wrong, Wonder Woman was probably the best part of the film, but without her, we wouldn't have needed something for the three of them to team up against. Without Wonder Woman we can lop out Doomsday and the other metahuman subplot entirely. We can go from "BvS: DoJ" to just BvS. With the extra half hour we saved we can further develop Bruce/Alfred, Lois/Clark, Lex/Supes, The Daily Planet, etc.
If they still insisted upon killing off Supes, Batman could've done it. He almost did anyway. The "Save Martha" couldve come after the killing blow had been struck. And then once Batman goes to save her, he has a conversation with her, where she explains how good her son really was. Upon watching a video replay of the battle, he sees Superman showing restraint and trying to talk Batman down. Batman sees how his rage took over. Killing Superman mirrors Zod's death from Man of Steel. Fans are obviously unhappy about this, but at least its a thematic parallel. And it would've been a surprise. Pretty risky move.
Then he goes after Lex, who he realizes was the catalyst for the entire battle. He stops him before he completes Doomsday. Sends him to prison. He then reviews the metahuman data recovered from Lex's archives (during the end credits) and decides to unite the JL. He also sees the Zod resurrection project (a nod to superman's revival).
Maybe, idk. I'm high.