The Superman reboot has to be a character-driven story arc with mature undertones for adult audiences. It should be a personal story filmed on an epic scale. Which means that the first part of the film should explain his motivation for becoming "The Man of Steel" and how his early life leads him to build a code of justice and humanitarian service.
Part I
The first part of the film should emphasize Clark Kent at his most apathetic; squarely in adolescence, at an age where he remains bitter, insecure, and unsure of his place in Smallville.
At a young age, he is taken in and adopted by a Midwestern couple, Martha and Jonathan Kent, who raise Clark with their "All-American" son. His adoptive family work tirelessly to provide a wholesome and "normal" childhood, but he continues to feel something of an outsider - living up to, but unable to fully understand the values of his "home." He is a nervous, bumbling, seemingly dimwitted boy who makes several attempt to blend in - only to fail. Well aware of Clark's physical gifts and talents -- and yet concerned for his safety -- Jonathan angrily prohibits his adopted son from using them. While encouraging him to remain indoors whenever possible, Martha, the more affectionate mother, stokes Clark's love of reading and writing. Suddenly, an incident occurs between the two boys, where Clark's brother dies, and Clark cannot to save him -- unwilling to use his powers at a crucial moment when they are needed. His relationship with his parents quickly deteriorates, and Clark blames himself for the death of his brother. Burdened with guilt, and convinced that he will never be able to accept him for who he truly is, he enters a pilgrimage, traveling the world seeking to find himself -- only to run into constant injustice aimed towards the powerless. Disappointed and disillusioned by what he witnesses, he arrives in Alaska - at one of the most northernmost, and desolate points of the country. Here, in this self-imposed exile, Clark meets a blind man who's condition is an exact opposite of Clark's -- blind and physically weakened by years of unrewarded service, but whose wisdom and boundless optimism greatly inspires a young and cynical Clark. Clark assists the man in his day-to-day life, while the man assumes the role of a sage (who conveniently is unable to witness Clark's superhuman powers at their most unrestrained). During the prolonged darkness of artic winters, the lack of sunlight deprives Clark of his powers and drastically weakens him to the point of near-death. The blind man, whose sight is always nothing but darkness, takes care of him during these crucial times, teaching Clark the values of self-reliance, humility, patriotism, cheerfulness, and courage. Soon, he is able to muster the strength and will to preserver at his most weakest. This experience helps forge Clark's identity as he finally learns to forgive himself and overcome his self-doubt, all while sensing his potential to do good against injustice. By happenstance, he comes across a patch of ice that seem engrained with an unusual "S' symbol...
Clark returns to a Smallville he no longer recognizes: rural America in the Post-Industrial World. Lexicorop is monopolizing agriculture and putting families out of work, homes are being foreclosed, a meth epidemic has torn the community apart, and ethnic tensions are running rampant over immigration. The residents of Smalltown are no longer able to recognize Clark Kent, and are amazed when they hear of his escapades and his sudden interest in becoming a journalist for the public good! His parents, amazed by the radical change and his personal growth, finally decide to reveal the secrets of his arrival on Earth. He is handed a Medallion bearing the unusual "S" symbol. Clark is unsettled, until he realizes that the device is key to literally "unlocking his past." He returns to Alaska to find that the Old Man has vanished -- his home and the surrounding communities have been uprooted by Lexcorp oil drillers. Clark uses the device to discover his "Fortress of Solitude" and message stored by his parents.Inside, a hologram of Clark's father appears; Jor-El explains his origins, Krypton, his parents, about how his planet was destroyed and how hes supposedly the last of his kind. He also tells Clark about his powers and responsibilities to protect Earth and humankind from the same fate. Also, Clark learns that the "S" symbol is his family's crest, symbolizing hope for a the future. Inspired, Clark finally is able to come to terms with his past and his alienating powers -- realizing that he was brought to this world destined to do good. His acceptance of his past and who he is, empowers him to become Superman.
Part II
In this part, Clark evolves into the Vintage-Superman of 1930s -- the "Defender of Truth and Justice" echoing the liberal idealism of Franklin Delano Roosevelt's New Deal and fighting for social justice against tyranny. Clark enters Metropolis, just before a Katrina-Style Hurricane is due to engulf the city. The city's establishment, enamored in wealth and prosperity, is caught woefully unprepared and its neglected citizen's left utterly defenseless. Till now, Clark -- an up-and-coming journalist for the Daily Planet -- has stood by and watched the city's poorest suffer. Finally, he summons up the courage to bring relief to the victims of the hurricane - donning the emblem of his homeland as a coat-of-arms and tribute. He emerges from the natural disaster as a public hero known as "Superman", who crowds hails as someone who can bring the city back on its feet. As Metropolis struggles to rebuild itself amid rampant crime, political corruption, corporate greed, bureaucratic incompetence, and ethnic distrust, Superman seems to be the only one willing to step in as a social activist. Throughout the film, he fights crooked businessmen and politicians and demolishes run-down tenements (a la vintage superman).
Against this backdrop, he antagonizes Lex Luthor -- a charismatic businessman, famed inventor, revered philanthropist, and so-called favorite son", who thinks of himself as the ultimate hero and humanitarian... until Superman arrives to steal his glory. I like Chiptooth's description of Howard Hughes and Gordon Gekko as possible influences for his eccentric mannerisms (Hughes) and vain, unemphatic personality (Gekko). But my preference would be to portray Luthor as a cunning, sardonic, morally-ambivalent manipulator who has used his influence and money to shape Metropolis' political climate with impunity. As Metropolis' "favorite son", he promises to rebuild the city with advanced technology and new industries for economic growth. And yet his disregard for ethics undermines any hope for a just and honorable recovery...until Superman arrives. Unable to bribe Superman or place him in his "pocket," he is determined to uncover the truth behind him and mounts a campaign to have his "vigilante tactics" outlawed. Luthor soon becomes a vocal critic against Superman, cautioning the public against such a powerful man, and using his political and underworld connections to turn the city against him. His obsession stems from his misguided reactionary attitudes towards Superman (e.g. he firmly believes that an extra-terrestial presence is a danger to humanity) and his love of power and the status-quo.
Also, in a reboot, I'd like to see the traditional dynamic between Superman/Clark and Loius Lane as a hardened "tough-as-nails" journalist attracted to Superman, but displeased with her new journalistic competition in the form of Kent. In my vision for a reboot, Louis is investigative journalist and whistleblower of Lex Luthor's questionable business practices and corrupt influence on Metropolis. She is a successful journalist who has received numerous awards and offers from more prestigious papers, and even proposals to appear on television with her own show. Still, Louis decides to stay with The Daily Planet, cause she sees it as the "last honest act in town" and the only remaining bulwark against the city's crime and corruption. However, like much of the journalism industry, the Daily Planet suffering from financial woes, and Lex Luthor (who controls the local media) is threatening to take-over the publication and use it to further glorifying his positive public image. While still being portrayed with the traditional straits of her character (strong, opinionated, yet sensitive) I don't want her to be the damsel-in-distress, but moreso an assertive and passionate woman who finds herself inspired by Superman's arrival, and perhaps motivated to persist in her own cause to save the Daily Planet against Luthor, who increasingly resorts to using his criminal connections to intimidate her and the paper's editors.
At the risk of generating controversy, I think it would be cool to have Lex Luthor be responsible for the collapse of the levees (them having been built by Lexcop, and him knowing that they were inadequate) as an attempt to destroy the city and re-build it with lexcorp being the #1 in the town, and Lex being hailed a hero for helping rebuilt it. Lois would be the investigator who uncovers this, and Lex would attempt to have her killed before she write her damming story.
Also, I want to portray Lana Lang as a Senator or public figure of sorts (...I'm thinking the Mayor of Metropolis!). While still a political animal, she could be a figurative extension of Smallville, who, like her small hometown, finds her integrity under siege and compromised by Lex Luthor's influence, until she summons up the will to stand up against Lex Luthor at the risk of losing her career. You could tinker with these factors to make for an interesting plot (perhaps stoking up Lana's and Clark's romantic tension - and inserting Louis in the mix) but in the in the end of the arc, Superman should be deputized as a legitimate agent of law enforcement, and Lex Luthor's public image as an honest and respectable businessman and pillar of community is shattered (although he manages to avoid imprisonment while he plans for his revenge on Superman - paving the way for a sequel!).
Part III
I haven't been able to write up a premise for the climatic part of this arc, but Superman needs a opponent that not only challenges his physical strengths, but also his core beliefs towards humanity. Brainiac would be perfect (armed with Kryptonite of course!) but he cannot be some plot device that brings forth action and special effects. His mission should be to destroy Earth, but he recognizes Superman as both an obstacle and potential ally. In return for his aid, Brainiac not only offers Superman the chance to become closer with his homeland (supplying him with his pocket-dimension virtual-reality of Krypton) but reveals that he may not be the last of his kind after all. He offers him assistance in reuniting with those who escaped his planet's destruction, and will spare the Earthlings of his choosing (provided that Braniac could keep them as part of his collection). Brainiac ought to be a reminder of the world Clark has lost, and perhaps he could be seen as a foil -- Superman as his polar opposite would be -- one that is the embodiment of Nietzsche's "Superman" -- a cold, calculating alien who has transcended the limitations of society, religion, and conventional morality to become a force capable of destroying entire planets. Clark, on the other hand, discovers himself as an alien, gifted with incredible powers, but who chooses to honor and ultimately defend human moral codes in the name of good.
Brainiac should be capable of messing with Superman's psychologically, by poising a moral dillemma regarding his ideals, past and origins. Perhaps Brainiac tries to conjure up pictures of Jer-El, trying to convince superman that Earth is not worth saving, because men like Lex Luthor will always remain in power and inflict injustice, and that whatever Superman does for humans, they will never accept him as one of their own. Of course, he resists, and fights an epic battle. In the end, Superman transmits a message to all surviving Kryptonites in space, telling them that they have a new home on Earth.