The Golden Compass had much more potential than the film that was delivered. The film was originally scripted pretty close to the book and was supposed to end on a fairly dark note. But since New Line saw it as a franchise, they decided to cut the ending to keep it family friendly and completely restructure the movie. The result was not only a poor movie but one that failed to bring in audiences and even alienated fans of the book.

Star Trek V was pretty much destroyed by last-minute budget cuts. I still like it, though.

I'm not sure of the intent of the OP ... but since you mentioned Kingdom of Heaven - I point to it and The Abyss as shining examples of what a director's cut should accomplish. The studios stepped in and completely removed key plot points that left the movies neutered. After finishing the theatrical cuts I scratched my head, knowing that something was missing.

Incomprehensible? Surely you jest.

At least we would have been able to tell the sex of Foster's kid. I was halfway through the movie before I realized she was a girl.

The theatrical voice-overs-added version of Blade Runner.

I thought the same thing, but she's all woman now.