So, Lex Luthor somehow manipulates Batman and Superman into fighting, steals what looks like the colonization ship that was crashed on earth from the first movie, as well as Zod's body and all the remains of kryptonian technology. He then creates Doomsday, and sets him off to rampage, forcing supes, Batman and Wonder Woman (and Cyborg and Flash and Aquaman also, apparently, all rumored to be appearing in the movie, with only Aquaman confirmed) to have to stop him.
How do we fix this shitfest? Well, right off the bat, nix Doomsday. I don't care if they're planning to carry him over into Dawn of Justice Part 2 or whatever, just get rid of him, it's way too early for Doomsday. Marvel didn't blow their load and put Thanos in the avengers, it's been building up to that, and so too does Doomsday need to build.
Also, Luthor manipulating Batman and Superman into fighting just makes them both look dumb. Instead, Luthor, who is a brilliant mind that's now become obsessed with kryptonians now that he's seen their power, collects all of the remains of kryptonian technology and starts to experiment with it. In his experimentation, studying the genes of Zod (bred specifically to be a nonstop warrior) and the remains of the alien technology, manages to create kryptonite, specifically red kryptonite. The red kryptonite is how he plans to manipulate Superman, pitting him and Batman against each other just because he can, because he wants a kryptonian servant.
Maybe in his experimentation, he discovers it's also been affected him, but in a much more subtle manner. His hair starts falling out, he starts developing health problems, but his mind moves even faster, he gets even smarter... Luthor is (thematically) the opposite of Superman, using cunning and intelligence as opposed to super brawn (yeah, I know Superman is also super intelligent, shut up.) This helps to set him up for a bigger role in a future movie, might even lead to him building a robot suit, I really like robot suit Lex, I don't know why.
Alternatively, instead of red kryptonite, he could still go the 'create a kryptonian clone' route with Zod's genes, but also include Superman's DNA and create Bizarro, with the aforementioned kryptonite used to imprison the real Superman.
Ultimately, I think the villain of the movie should be an 'evil' uncontrolled Superman, because that's obviously the way they want to go, and it worked well in Injustice, but at the same time they need to keep Superman's moral integrity, or what little there is after Man of Steel, because he needs to be the hero in future movies.
These are just spitballed ideas, but they all sound way better to me than Batman and Superman being dumb and then Doomsday gets farted onto the screen.
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