Here's what I would do, personally at least.
1.) I would open the film with a precredits sequence of a fight from later in the film where Superman is having trouble. He's about to fall unconscious.
2.) The credits sequence would be in the form of flashes. It wouldn't show his origins but would be more along the lines of showing his childhood. When the credits ended there would be a photo of his leaving Smallville.
3.) The story would open with Clark arriving in Metropolis and starting at the Daily Planet. When he arrives he sees a woman almost get hit by a car and pulls her out of the way. He would be hired, barely, by Perry White because he owed his parents a favor. I would incorporate one thing from the Smallville continuity only: Martha Kent became a Senator and that's the only reason why Clark got the job at the Planet.
4.) I'd introduce Lois as being off on a story (she'd also have been the one that Clark saved from getting hit by the car by pulling her out of the way). She's working on a case involving the mob and has infiltrated the Intergang. She's gained a lot of power in the gang and is close to meeting their leader (Morgan Edge), this is one of her first major stories after being promoted from the obit beat, but her major contact in the gang (Leslie) is murdered for being a police informant. Lois takes her place because Edge doesn't see her as a threat.
5.) Clark finds the dead body of Leslie and takes her to a hospital. He scans her, using his X-Ray vision, and sees that her heart is still beating very shallowly and that she has a pulse. He takes her to Metropolis General where she's being attended to by a doctor and his assistant (Emil Hamilton). The doctor declares her dead and takes her to a laboratory where he begins to experiment on her dead body; the Doctor is in the employ of Intergang who payed his school bills.
6.) Clark, superspeeding through Metropolis, starts to realize just how badly things have gotten in the town and starts to wonder if he should use his gifts to help others as, almost, a full time job. He returns home to Kansas, briefly, to talk with his parents. His mother and father are still alive and they remind him that they'd spent their entire lives trying to keep his history secret - even spending a lot of money to forge his birth certificates so that it looked like he was really their child - but they respect his decision and tell him to do what he feels is best. Even though they are still farmers at heart the Kents are a very modern people.
7.) In Metropolis Lois is busy with her case when she makes a big discovery: Morgan Edge isn't the leader of Intergang like she thought. But she's making incredible headway into the organization and has become a lieutenant in a very short time. While she's at a club owned by the gang she watches as three of the intergang's members are killed by what appears to be electrical shocks. Lois swears that she sees Leslie for a moment but explains it away that she's just in shock.
8.) Perry tells Clark to write about the deaths at the club and he's intrigued by what he reads about how they were all killed through extreme voltage going through their bodies (which isn't possible from simple faulty wiring like the physicians claim). He decides, on his own, to go investigate the club and finds that the wiring is normal. While there he runs into Lois and is instantly attracted to her. He asks her out but Lois rebuffs him saying she can't stand reporters and challenges him that he only got his job because of his mom.
9.) Later that night Clark, who has worn glasses since childhood, decides to let his powers wander and hears a crime nearby. He decides that it's time for him to fulfill his destiny and becomes Superman. This is similar to the costume to the left in my avatar box (he hasn't made an actual costume yet) and incorporates a trench coat instead of a cape and dark blue exercise equipment. Before he leaves he quickly attaches a logo that he created in childhood - an S in a diamond shape - to the chest by sewing it in place. He saves the woman, a fellow reporter named Cat Grant, from her attacker and goes to help others in the city. This would be similar to the montage in Superman Returns. Then he hears another scream and it turns out to be Lois. Superman goes to her and finds that she's alone but he senses severe electrical disturbance.
10.) The next morning Clark goes to work and is surprised that Lois is there at her desk (he hadn't officially met her yet). They talk, briefly, and Lois fills him in on everything and about Leslie and her death and Lois' case. She details everything she's learned about Intergang and it would be intercut with scenes of how she got started with them.
11.) Lois, after leaving the Planet, is followed by Kyle Abbot. He kidnaps her and throws her in the trunk of his car. As they're driving Lois hears screaming in the car and what sounds like electrical buzzing. A second later the car crashes and Lois awakens in the hospital under the care of Emil Hamilton. He explains that she appeared at their door mysteriously and that a man had been sitting there since she arrived. She looks out the window and is surprised to see that it's Clark. She doesn't know how he found her or knew how she was here. Though she knows, deep down, that he had something to do with her being rescued.
12.) Clark talks to Lois about the car accident, he was of course who rescued her but denies it saying he was at the hospital to meet with a Doctor about his story. She explains that she heard buzzing and screaming in the car before it crashed. Clark knew this and already investigated, finding electrical burns in the front seats and on the body. Later he talks to Hamilton and asks him, as a journalist, about the dead man brought in with the limo. He explains that it was the other Doctor, Doctor Thaddeus Sivana, who handled that case. He was the same Doctor that declared the Intergang members dead and Lois' contact Leslie. He hasn't been to work lately. Lois screams claiming she saw Leslie in her room and that she disappeared. Clark scans the room and senses the same traces.
13.) Clark, as Superman, tracks Doctor Sivana to a secret laboratory beneath the hospital. He goes to question him when he's attacked by Leslie AKA LiveWire. This is the scene from the beginning of the film. Superman gets a second wind and is able to contain LiveWire through Super breath and his electrical vision and goes for Sivana. Superman questions the Doctor using some Batman inspired techniques - to an extent - until he finds out that Edge has known all along about Lois and was using her to find the traitors to the organization. This was all concocted by Edge to impress his boss as he's not the real leader of Intergang. Sivana has no idea who the big boss is.
14.) Superman goes after Edge at his Penthouse. They fight but Edge has an advantage. He uses and antique knife he has kept at his side since he was a lowly initiate and the knige has a unique effect on Superman. It can slash through Superman's aura because the handle contains a mystical element. Superman is able to stop him, in time and through creativity, and Edge is delivered to Police Headquarters with all the information that the police need to throw him in jail. He's arrested by Police Officer Maggie Sawyer.
15.) Morgan Edge is with his attorney minutes later and the two are talking about his defense. He tells the mob attorney - who is supposed to be a lieutenant Edge himself brought in - that the big boss will take care of him and the attorney tells him that the boss isn't happy. The attorney assures him though that they'll have him out soon enough. The attorney leaves and Edge, realizing he's not going to be helped, asks to speak with the DA. He wants to make a deal and he starts coughing.
16.) Clark and Lois share the story with Perry being convinced that the two will share a Pulitzer for their work. Perry, who was intrigued by the stories Edge was spouting as he was captured by the police, has tasked the duo with a new story: they're to find out the truth about this mysterious 'Superman' that Edge and even Cat Grant had talked about. They're teamed with a hot shot young army photographer back from Iraq named Jimmy Olsen. Lois tells Clark that he may not be as bad as she thought, but that he was still only there because of his mother. Instead of being offended, Clark instead laughs.
17.) Edge's attorney walks into a lavish office with an incredible view of the Metropolis Skyline. He walks to the desk and a man sits staring out the window. The attorney tells him that it's done and that Edge won't be a problem any more. They attorney, to show his allegiance, spiked Edge's water. The bald man, Lex Luthor, turns in his seat and says that Edge is immaterial as they have a new threat in the form of this mysterious Superman. Luthor tosses the computer monitor with the camera feed of Superman on it and vows to destroy him no matter the cost.