1- I would include a dream sequence before Clark wakes up on the farm . A brief montage of Superman exploring the remains of Krypton, as he passes through the valley of elders and imagines how it was in the glory days of Krypton, people being happy, children playing on the streets, Jor-el with baby kal-el and his wife at home(scenes from superman 1) and then everything turns to black as is being taken away from him as he wakes up and all we see is the stars in the ceiling of Clark`s bedroom. This is a nod to "the man who has everything" story and shows Clark loneliness in the universe. This would show how painfull the return to Krypton was for him and improve the theme that he is looking for some place to belong. Now he is at Earth, alone. So, later in the movie, when he "eveasdrop" Lois, people would understand that he just want to be a part of a family.Also, it is a nice set-up to the conversation with his mother next morning. Also, its a sin the this sequence will see the light of the day only in the DVD. This way i`d show just a little bit of it, making it revelant. No need for 20 mins of him exploring the remains. Just 2 in this brief dream sequenece. Singer, imo, commited a great flaw to cut everything.
2-Cut the "whole place was a graveyard" line - I thought this line was bad delivered in the movie. It might work on the paper but it doesn`t in the movie. In a movie, you`re not supposed to talk about important plot momments. You have to show it. Since i included the dream sequence, this line wouldn`t be needed.
3- Include "not even you cant stop the world from spinning" as he watches the panic of the real world on tv and his mother reassuring that the world needs a Superman. Martha and the Kents were way underdeveloped in this movie. Superman is who he is, human, not because of Jor-el but the Kents!
Just 3 simple changes. Adding what? 2 minutes to the running time with the dream sequence. It would make the movie MUCH better, make the themes of the movie easier to understand and more cohesive.
Superman Returns is not a classic because of these small flaws. Singer had great ideas but "not as great" execution in key scenes.