What Could Have Been: Word of God says chapter eleven wasn't originally going to be from Mew's point of view, but there was a given option of rewriting the entire chapter to literally project Mewtwo into the past and not in her head on request if it proved too confusing to the reader.
What Could Have Been: The original editor's cut of the film was more than twice as long, and included a B plot that paralleled the relationship between John Henry and Mary Alice. The final cut focuses on the relationship between John Henry and his father.