Literally Flint, take out those moments with Martha and Lois that are meant to "force the fight" and the film would work much better. This motivation wasn't even needed for them to square off after the great setup they did at beginning of film!!! Superman already had that talk with Batman about the Bat signal, they have different philosophies, etc... That was enough. Superman showed him mercy the first time. They'll square off because Batman was prepared to whoop on him anyways. Omg it almost makes me angry how they piled on unneeded story elements.
The Lex moments and silly kitchen timer, the countdown of Martha to be [blackout]"killed" [/blackout]was just unneeded cliches of heightened stakes added on to the ending. Lex should have been manipulating from his office in first appearance anyways, not getting jailed for getting so involved with every major player character. For him to get jailed right away, rather than just using others makes me feel like Snyder doesn't get what has made the modern take on Lex so great.
Lex could have been working with the government, even a brief scene or two with Waller explaining intent to create a defense mechanism such as project "Doomsday" from him and his scientists after the events of MOS. Doomsday releases from the lab, and trinity comes together.