In the many changes that the original plot had, the most dramatic changes are: In the anime, when the girls are in an elevator, Asuka slaps Rei for their passivity, while in this film, she tries to slap her and Rei stops the slap with her hand. In the series, Shinji only threatens to destroy the Geo-front, in the film, he does manage to meet this threat and he is seen destroying part of the Geo-front. Toji's younger sister is seen fully recovered in the film, but in the series, the fate of her is never know. In the film, Asuka is much more open with Shinji. For example, the scene of the series in which she lies beside him, she falls asleep and Shinji moves away, but the film she stays in bed and they counted each other's fears, with greater harmony between them that at other times. In the series, when the EVA-01 match against Zeruel, EVA-01 goes into Berserk mode alone, while in the film, Shinji does so at their own will. In the the series the EVA-01 also rebuilds the lost arm with a piece of Zeruel's ripped body, while in the film, the EVA 01 creates a sort of "condensed energy arm" which is also used as "cannon momentum" against Zeruel.
Asuka appears in this film, with a change to her name: it goes from Soryu to Shikinami (in Japanese means "Spreading Waves"). In this tetralogy, and it was said after the premiere of the film, the character of Asuka experiences significant changes in personality. In this film, she has no aversion to dolls. In fact she has a glove puppet that talks from time to time, using it to wish each other luck. She says to Shinji that is a reminder of his mother. She is now referred to as holding the rank of captain. She is also no longer infatuated with Kaji, choosing to ignore an invitation to go on a trip with him, until Misato forced her to go. In addition, she tested unit-3 instead of Touji, but she manages to survive the Bardiel incident, as she is seen with an eye patch in the preview image sequence at the very end of this movie.
The character, Makinami Illustrious Mari, is a secondary character entirely created for this film. she is not from the original manga or the TV series. Yoshiyuki Sadamoto designed her to look British, and added glasses as a 'simple yet effective way to set her apart from the other characters'and continuing the tradition of using names based on ships of the second world war, Makinami is the name of one of the destroyers of World War II Ayanami class. together with the Shikinami and Ayanami destroyers, who served in the Imperial Japanese Navy. Also Illustroius was a class destroyer ship used in World War II, serving in both the U.S. Navy and in the English navy.
Continuing with the tradition of using religious references, in this film is invoked the "Vatican Treaty" where Japan and all other nations are forbidden to possess three or more functioning Evangelions at a time. The Unit-01's dummy plug system is manufactured at Golgotha Base, which is named for the hill (also known as Calvary) where Jesus was crucified.
The release date was pushed back several times from the original announcement of January 2008: first, to a December 2008 release before an update on the official website on October 6, 2008 announced the official English title and a "early summer 2009" release date. A final postponement revealed that the film would be released on June 27, 2009.
Mari the Illustrious wasn't originally intended to appear in this film but rather in the third movie, Evangerion shin gekijôban: Kyu (2012). It was because of overwhelming fan-response to her appearance in Evangerion shin gekijôban: Jo (2007) that producers decided to expand her role for this film.
The new Asuka's last name comes from the Japanese destroyer Shikinami, Yard number: Destroyer No. 46, Laid down: 6 July 1928, Launched: 22 June 1929, Commissioned: 24 December 1929, Struck: 10 October 1944 and sunk in action in 12 September 1944. The older last name "Soryu" came from the "Japanese aircraft carrier Soryu" one of the famous aircrafts Sunk by air attack at the battle of Midway in 4 June, 1942.
Originally it was planned that Asuka and Mari would pilot Eva Unit 02 together during the battle with Zeruel. In the final film Mari pilots it by herself since Asuka is hospitalized. The scene was storyboarded but not filmed.
The trivia items below may give away important plot points.
In the series, along with the fact that Rei was originally going to die, Zeruel didn't take on a humanoid form (although at that point, the Angel had consumed Rei and half of her Eva in the film). Also, in the film, saving Ayanami would result in starting the Third Impact, unlike in the series, Eva-01 only went berserk and began to eat Zeruel.