I'd do a full reboot of Superman. And it'd go a lil' something like this:
Man of Steel: It's basically Superman's origin story. We start with Clark Kent arriving in Metropolis and getting his job at the Daily Planet. This is followed by several mysterious reports of a flying "Superman" saving lives all over the city. We get a few scenes with Clark talking to his parents, with mention made to how he arrived on Earth. We then see Lex Luthor, billiobare CEO of Lexcorp and genius innventor, taking an interest in these Superman reports. He tries to contact Superman by faking a disaster to draw out his atention. He offers Superman a partnership, saying that they could reshape the world into a finer place. Superman says quite flatly that he is not interested, and it becomes quite evident that their philosophies are very different. As Superman, Clark starts up a rather unique relationship with his partner in the news room, Lois Lane. He comes to he, floating outside of he window at night, and talks to her, using her as his way of getting his voice out to the people (and avoiding any suspicions that may rise if Clark Kent served this role). Lois becomes infatuated with Superman, but their relationship in this is a bit more distant, him serving a sort of gaurdian angel role. Meanwhile, Lex starts setting up several tests for Superman, including faked terrorist atacks and the like, to judge the level of Superman's power. Superman overcomes these obstacles, but ends up bleeding a little bit from one of the encounters. Lex takes the blood sample and has his scientists grow a clone. They succeed, but the creature is imperfect. It is mentally under developed, and lacks any skin pigmentation. Still, Lex orders the creature to kill Superman and take his place. This leads to a massive fight between Superman and his clone, which ultimately results in the clone dying in an atempts to shut down a nuclear metldown, which he and Superman accidentally caused during their fight.
Last Son: Clark begins to try and realy dig into where he came from. He begins looking over his ship, but to no evail. So, as Superman, he taked his ship to Dr. Emil Hammilton, a scientist in Metropolis. Hamilton looks over the vessel, and is soon able to activate it. Clark hears the voice of his father, Kal-El, telling him that the computer program within the ship is modled after his (Jor-El's) consciousness, and is in essence him. Superman begins learning all sorts about Krypton's history and culture from "Jor-El," and begins to reflect on how this effects the humanity that he always felt he had until learning of his heratige. Soon, "Jor-El" begins talking about remaking Earth in Krypton's image. Superman objects to this. Not only would terraforming Earth to be like Krypton's environment and altering the humans genetically to be essentially Kryptonian in nature kill millions, but to reach Krypton's state of near utopian status, which happened after centuries of technological, social, and political developement would require enslaving the human race and forcebly bending them to Kryptonian ways, which would also result in countless deaths. Fearing what "Jor-El" might do, Superman shuts the ship down. However, the ship reactivates itself, and using the technology in Hammilton's lab builds itself a superhuman body. It is revealed that "Jor-El" is in fact The Eradicator, a Kryptonian military defense program. Jor-El coppied a variant of it into his son's ship that was designed to protect Kal-El and preserve Krypton's culture at all costs. Over time, the programing evolved, and is now willing to count mass genocide under "all costs."
Th Eradicator flies to the North Polse, where it begins the terraforming process. Superman follows, and tries to stop the machine. It initially atempts to merely contain Superman, as his programing includes protecting him. However, as Superman proves very dificult to contain, The Eradicator reasons that beating him to within an inch of his life and allowing him to heal while it completes it's work wouldn't be against his programing. Anyway, massive fight insues. It goes up into the upper atmosphere, where Superman defeats The Eradicator by tearing out it's "brain" and throwing it into space. He then flies back to the north pole and ends the terraforming process, which leves a Kryptonian-like structure in it's wake.
Brainiac: A probe in deep space, having taken notice of the actvity on Earth in the previous film, comes to Earth. It locates Milton Fine, a low level telepath/telikinetic and stage preformer, and kills him, taking over his body and altering to better suit it's purposes. It then takes Fine's stage name, Brainiac, as it's own. The probe had been built on the planet Colu, a planet run entire by computers (ala the Borg), to spread the peaceful nature of Colu to other planets. Brainiac goes to Metropolis, wanting to use Lex Luthor's technology, in conjuncture with the Kryptonian technology in the North Pole, to create a means of "pacifying" the human race and then spreading it's influence to the rest of the universe. To help, it creates two superhumans, Metallo and The Parasite, to serve as his workers. It, of course, does not tell them the true nature of It's plan. When Lex becomes aware of what is going on, he contacts Superman, who has already fought Parasite and Metallo twice as they go about stealing technology for Brainiac. Lex and Superman go to the North Pole, where Brainiac is readying to pacify the planet. Lex easily defeats Metallo by shorting out his systems, and Superman finally beats The Parasite, who had constantly been bragging about how superior he was to Superman, by freezing him in the arctic snow. There is then a huge battle between Brainiac and Superman. Superman, however, is unable to defceat Brainiac, only stalemate him, as he soon realizes that the only way to defeat him is to kill him. Lex, however, is fully willing to do this, and shoots Brainiac in the head (it should be noted that Brainiac's powers are completely psychic/energy based, and as such his body isn;t too much more durable than that of a human). Lex then takes Brainiac's body back to Metropolis.
The Elite: Lex, using cell samples from Brainiac's body, creates a team of heroes that he thinks are better suited to save the world than Superman. They are The Elite, lead by street wise British hoodlum Manchester Black. The story follows pretty much follows Action Comics #775, with aspects of Lex Luthor: Man of Steel thrown in to expand the plot. This is very much a Lex Luthor film, and some elements of Lex's backstory, taken from Lex Luthor: The Unofficial Biography, will be mentioned to help flesh out his character. The story ends first with the ending of Action Comincs #775, with Superman defeating The Elite and giving his speech about how extreme methods used to save the world are unnecessairy, and then with the ending of Lex Luthor:Man of Steel, with Lex talking to Superman through his window.