Superman Returns/WMG

Lex Luthor is Keyser Söze
Same 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.
 * According to the Blue Book of Pianos the average Steinway Pianos weighs between 540 lbs and 990 lbs depending on model.
 * Lex Luthor bought a custom, ultralight weight piano so he can push it around easily and pretend he's Superman.
 * Seriously though, has anyone done the math on this? If Richard and Lois (and therefore everyone else) genuinely believe he's Richard's son... it's a pretty small window of opportunity, is what I'm saying.
 * I don't think they DO think that he's Richard's son. It's more realistic to think that Richard met and fell in love with Lois while she was pregnant. The two got engaged, they put Richard's name on the birth certificate, and no one cared beyond Jason now having a father.

Superman Returns is set within the Burton/Schumacher Batman universe.
Superman and Metropolis are mentioned in Batman and Robin and Gotham in Superman Returns. Plus after Batman Returns the events of Superman Returns take 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
 * Either that or Superman's sperm has rejuvenating qualities.

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?