1) Superman II
The most famous example of a superhero movie completely changing during production has got to be Superman II, whose behind the scenes turmoil has become cinematic legend.
Initially, the plan was to produce Superman and its sequel in one go, with Richard Donner overseeing both at the same time. However, due to problems between the director and producers Alexander and Ilya Salkind, Donner was removed from the sequel and Richard Lester was brought in.
Unlike all these other films, though, we actually have an idea of what Donner’s version would have been like. 2006’s Superman II: The Richard Donner Cut saw the director re-edit Lester’s film and add in his own scenes that didn’t make the theatrical cut, like the inclusion of new footage of Marlon Brando as Jor-El and Superman’s tragic climax being transplanted to the sequel, as was Donner’s original plan.