The reason it’s almost impossible to make a good Superman movie is because Superman is perfect. Not just physically, but morally. If you take that away, you take away everything that makes him Superman. The first two movies worked because the first was about him discovering his abilities and the second was about him facing a moral dilemma, choosing between Lois Lane and his duty as Superman. The fact is, his idealism is why people like him. So instead of changing him, why not change the world he inhabits? Instead of the cold war era moral certitude that went hand-in-hand with “truth, justice, and the American way,” put him in today’s society.
At what point is he overstepping his boundaries? Would a real-life Superman be morally obligated to overthrow brutal dictators? What good is having a nuclear arsenal if one man can stop all your missiles single-handedly, and you can’t hurt him? Who is he accountable to?
The story would be the logical progression from the first two movies. Part 1: Superman hones his ability, and becomes a force for good. Part 2: He decides to dedicate himself to his position as Superman, instead of his civilian life (including personal relationships). Part 3: He learns the limits/consequences of his actions.
The story would start with Superman coming back after years, maybe decades, of absence (I know Superman Returns did that, but bear with me). So he gets back (having aged much less than an average person), and everyone is understandably excited. But the world is drastically different. He would stop a military action against civilians in a stand-in for Syria, and the international reaction would be extremely negative. The military will be trying to stop him, and will contract out to Lex Luthor to develop technology for a contingency in which Superman would need to be killed/contained. The big thing would be the moral quandary for Superman. Even at the cost of alienating governments, and in the face of plummeting public opinion, should he do what he thinks is right? He has to come to terms with the god he could be.
Luthor’s plan would pay homage to the original Superman movie. He would be secretly selling a nuke and guidance system to a North Korea stand-in. However, unbeknownst to the Koreans, the guidance system would allow Luthor to remotely launch the nuke, and crash it into the San Andreas fault. Not for beachfront property, but to cause a disastrous earth quake. And the only construction firm big enough and prepared enough to take over the government contracts for a reconstruction project are owned by Luthor, making it a multi-billion dollar payout.
Superman stops the nuke, but at this point, he’s completely disillusioned. Instead of sending the nuke into space, he hurls it back to a Pyongyang stand-in, destroying the city. When he discovers that Luthor was behind it, he goes nuts, and almost kills Luthor. Luthor makes some comment along the lines of “This is what you really are. You’re not a hero, you’re not even human.” And Superman lets Luthor live, if only to prove to himself that he can still hold that moral high ground.