Especially with the early rumors of the director's cut being 4 hours long, I think the movie should have been two parts. The first the Batman v Superman released on the original date in 2015, with more focus on Batman and Superman's differences. Since Supes worked with the army to defeat Zod in Man of Steel he could have been working them during this time, maybe having a little bit of a Dr. Manhattan like discussion and whether he should be used in combat not rescue missions and natural disasters. And Batman works with Lex in building the anti Kryptonian weapons. Bruce's paranoia could be due to Lex manipulating him with Scarecrow's fear gas, another way explaining why he's been so violent. The fight could end more like Dark Knight Returns with Batman feeling he made his point in just beating him and then Lois comes in to reveal how Lex was manipulating both Bats and Supes into fighting and them not able to arrest Luthor because they can't without exposing Batman's identity.
The second movie would come out on the actual release, March 25th. Here Superman keeps a protest in another country peaceful by just staying there. Superman wants to distance himself with the military and the U.S. so his actions won't be considered U.S. foreign policy, and the army wants to make their own Superman. Lex makes a Doomsday that he can control but slowly loses that control near the end. Batman is looking for other meta-humans and is close friends with Superman. Bruce runs into Diana, this time he's hacking into Lex's mainframe mainly to find the meta-human files on the other leaguers. Superman in the meanwhile could be trying to balance his civilian life with his superhero career and realizing how much he'll have to stop crime as Clark Kent when it comes to Lex Luthor and other wealthy people from Metropolis like Bruno Mannheim. Superman feels betrayed by General Swanwick when he finds out about Doomsday from Batman, and has to fight him when Doomsday goes completely out of control. The fight could go similar with Superman immediately taking him out to space and the DC Trinity fighting Doomsday together, that way his death would have more impact.