Deleted Scene: Many put back for the Richard Donner cut, while others were merely extras.
A bunch of scenes were shot for both versions, some of which went un-used in both versions, some of which were restored in extended TV cuts, such as a rather chilling scene (from the original theatrical Lester version!) of a young boy (the one who is supposed to be from the American mid-west yet talks with a British accent) being brutally killed by Non when he tries to ride away for help. This scene ends with an old woman exclaiming "He was only a boy!" to which Ursa cheerfully replies "Who will never become a man."
Executive Meddling: After almost finishing production on Superman II, director Richard Donner was fired by producer Alexander Salkind, who wanted a lower-budget movie with more Camp. The result on the franchise was disastrous — many of the stars, including Marlon Brando and Gene Hackman, refused to work with new director Richard Lester or participate in later sequels. It should be noted that however disastrous the result was for the franchise as a whole, the Lester version was still a critically acclaimed box office smash, and even Superman III enjoyed good box office (if not the critical acclaim) even if only because III piggy backed off the success of the first two films.
Donner had reportedly been at odds with the Salkinds from early on over the tone of the film and reportedly did not get along with Pierre Spengler, a long time friend and frequent collaborator of the Salkinds. Marlon Brando was said to have been cut out of the film altogether because he was too expensive, not just for his paycheck but because he got a big bite of the first film's box office and was entitled to a big bite of the second film's box office as well, which the Salkinds decided they didn't like. Jack O'Halloran, the actor who played Non, later accused the Salkinds of having done a poor job managing the budgets for both films.
What Could Have Been: Fans got a taste of this when the Richard Donner cut of Superman II was released (though it obviously wasn't as polished as it would have been had he been able to properly complete it). The "reversing time" trick was originally intended as a finisher for II, but Donner decided to use it as a memorable climax to the first movie. The directors cut restored it as originally planned, though Donner said he would have worked out a new ending if he was kept on.