Lex Luthor is Keyser SözeSame director, same actor, similar mannerisms, a penchant for disguises and aliases. It all adds up. The Usual Suspects is set in Bryan Singer's Superman universe. Keyser Söze is a myth invented by Lex Luthor to scare people, while Verbal Kint is a simple cover alias.
Jason was not Superman's son.That was just a really, really light piano.
Superman Returns is set within the Burton/Schumacher Batman universe.Superman and Metropolis are mentioned in Batman Forever/& Robin and Gotham in Superman Returns. Plus after Batman Returns the events of Superman Returns takes place. Lex Luthor's crystal continent could have caused damage not only to Metropolis but also (and maybe to a larger extent) Gotham. With most of Gotham in disrepair the city is completely renovated replacing all the gothic architecture with the bright neon lights shown in Batman Forever and Batman & Robin.
Lois Lane has the strange case of Benjamin Burton.30s years —-> 23 years
Jason, upset by the Parental Abandonment, will become a supervillain.Because reason to hate hero + superpowers + ostracized by peers = supervillain.
Lois Lane is angry at Superman because she thinks he raped her.Remember, Superman erased Lois's memory of their time together with his amnesia kiss in Superman II. To Lois's perspective, she never had sex with Superman or anyone else, but she somehow gave birth to a baby with superpowers. What else is she going to think?
Jason is going to become Superboy.Resulting in a universe with two supermen and a golden age of science and technology because Jason is being raised by his actual parent and will want to help his home world in a different way.
Brutus is the Killer Birthday Clown.Early in the film, Perry White mentions "that birthday clown massacre thing." Following on from this, Brutus has a tattoo of a scary clown face which the movie focuses on as if it means something. Ergo, Brutus is a former Monster Clown who murdered a bunch of people at some kid's birthday party. Which makes his... interest in Jason all the creepier.
Had Superman Returns had been more successful, the movie would have been the setup for a Justice League film.Think about it - Lex Luthor tries to create a continent in the ocean made out of Kryptonite, probably messing up marine life for thousands of leagues, and pissing off Aquaman. Gotham City is mentioned frequently in the movie - at one point, when Lex Luthor sets off his device, the map shows that Gotham City is not far from ground zero, so it too would have been affected, getting Batman involved. Depending on how far the Kryptonite affected the oceans, it could have affected the Amazons on their island, bringing in Wonder Woman to be sent as an envoy to the "World of Men". That leaves Green Lantern, Martian Manhunter and the Flash - perhaps one of the pilots escorting the Space Shuttle flight was Hal Jordan?
This film didn't have Kryptonite, but Tiberium.This explains how Superman could lift a whole island's worth of the stuff while still suffering some ill effects.