Looking over the Deleted Scenes, although I knew Singer had already said the "Return to Krypton" sequence would not be in the film, I was dissapointed the original "Return of Superman" with the change in the storage room wasn't on there either. I was also dissapointed that the plotpoint of Luthor fabricating the scientific reports of Krypton so Superman would leave were nowhere to be found. It really is amazing not only how much of this film was cut out, but how much of what was cut out was such a large part of the film's promotional material. I swear about half the trailers come from that alternate Clark/Martha scene.
Off the top of my head, the deleted scenes I would use would be:
-Clark waking up and going to bury the spaceship.
-The alternate Clark/Martha scene, with the baseball/Daily Planet transition to Metropolis.
-The alternate Lex/Kitty scene on the yacht. With the toupee and "Greatest Criminal Mind of Our Time" reference, it really ties in to the original films.
-Luthor's extended trek to the Fortress, where Kal Pen has lines!
-Lois naming New Krypton. This will probably be important in the sequel.
And I would absolutely cut the flashbacks of young Clark.