If I were gonna do this movie, I'd keep Lex, cuz, lets face it, Lex isn't the sorta villain that you can just put on the back burner. He's almost like a supporting cast member really. And if we're talking about an origin story, then he pretty much has to be present. But, he doesn't have to be the main catalyst.
With Lex, the thing they have to do is combine all the good things that make lex a good villain. He should be a genius, first and foremost. No insurance scam bulls**t, we're talking Super Science here. We're talking about a guy who has created things that could conceivably hurt, maybe even kill Superman. Second, the Businessman side. He's the smartest man in the world, with one of the biggest, and most profitable companies in the world. He should play this not just as a scientist, but as a ruthless businessman. Combining those two make for the perfect Lex. Lastly, we need proper motivation. Lex is essentially, the perfect human being. Genius on a level never before seen. A modern day da vinci. He came from nothing, and built himself up to become one of the wealthiest men in the world. After that, he went back to the place he grew up, Metropolis. This one horse town that was basically what would happen if you combined Detroit and Newark with a little more piss smell, and turned it into a thriving, wealthy city. Lex did this. This is his city. But, then comes this Superman. This, alien. This outsider, and he takes the city, and hell, the world by storm. Before he showed up, Lex was the pinnacle of human achievement, but what good is human achievement in the face of alien might? Lex, being the futurist that he is, sees the problem that Superman presents. He will be the death of man kind. He is a God, living among mortals. Already the sheep of Metropolis worship him, and it's only been a few weeks since he arrived. He will take Man's need to do what he must do. We'll become worthless sheep, dependant upon one being to do everything for them. He takes away the chaos that is life, and by doing so, he will destroy us all. It's Lex's belief that, he, being the only one that sees this, that See's IT for what it is, must somehow eliminate the threat, for the good of mankind. So, that's Lex's reason. Which is waaaaayyyyy better then some God Damn real estate scam. (What the hell were they thinking?!?) You can almost see his point.
The secondary villain, the muscle, the thing that Lex attacks Supes with would be Metallo. Lex wants to get a proper gauge of just how powerful the alien is, so, he unleashes the most powerful thing in his arsenal. He, through outside sources, hires a guy named John Corban to "steal" a weapon, lets say some kinda super advanced tank with energy beams or something. He does, wrecks much of the city, Supes shows up, Big fight ensues, Corban wont go down easy, ends up hurting himself badly. From this battle, Lex manages to get samples of Supes DNA, he tests a theory about something that he had come into possession of some years ago. A rock of alien origin. He exposes some of Supe's DNA to the rock's radiation and it destroys it. So, there's Kryptonite. Lex then uses the rock for what he was planning to use it for, to power a cybernetic frame made out of a synthetic and highly advanced metal he had Appropriated at some point known as Metallo. A super durable nigh indestructible ore that can absorb other metals into itself. (don't ask how, it's super science, best not to think about it too hard.) He then pays a visit to the paraplegic Mr. Corban, and offers him a chance to walk again, and get some payback on the man of steel. So, brain in the robot, metallo set loose on the city, big, big fight. Giant robot due to absorption of entire city blocks, Kryptonite laser beams, dogs and cats, living together, total anarchy. Supes wins somehow, Right before Corban can give up his accomplices, Lex fries his brain. So, in the end, all that destruction and death, and Lex comes out free and clear, but Supes knows. he knows it had to be Luthor. Can't prove it though. And end it with Lex and Supes having one of those classic starring contests where Supes floats outside his office window, and Lex tells him how he's gonna destroy him, and Supes is all, yeah right *****e bag.
that's my idea for the conflict of course. All that other stuff, mainly the Superman, Lois, Origin stuff can wait for another day.