I always felt Ritsuko was a very underdeveloped character in Evangelion. She will be altered significantly when she meets Akio just after her mother's death. At this extremely vulnerable spot, with her feelings for Gendo manifesting and the uncertainty of how to proceed weighing down on her, Akio will do what he does best: seduce her. In doing so, Akio gains an invaluable ally within NERV, someone other than Mikage who will know the truth of his intentions and who can more directly influence the training of the pilots without suspicion. Akio's affection will give Ritsuko conviction Gendo never provided her in Evangelion, and as such, she will become more than just his ally. Now passionate, she is his willing co-conspirator and lover.
By contrast, Akio needs Ritsuko, though he doesn't realize to what degree. Ohtori Kanae, his intended fiancÚ, does not survive the Second Impact. Anthy, his companion throughout many, many long years, kills herself and leaves him alone to live out eternity. After extensive work, he manipulates himself into SEELE, still hoping that it is possible to recover that part of him which was Dios. While Akio has a purpose in Rei's creation, he is utterly alone save for Mikage, when he seduces Ritsuko. Circumstances will not allow him to befriend and seduce Utena (or Juri) as he would like to. When Rei awakens to her power and rejects him, and later Misato kills Mikage, Ritsuko is the only one who has stood by him, his sole remaining confidant and lover. Though he does not love her as she does him, Ritsuko is nonetheless precious to Akio.
Asuka is going to have a difficult time. Despite the fact that she has graduated university at age 14, an elite pilot, and any number of other impressive statistics, her inability to best Juri in fencing is going to haunt her. In all the ways that it should be obvious to Asuka that she is better than Juri in many areas, Juri's superiority with a sword (coupled with the knowledge that Juri was NERV's most promising candidate and not her) will remain at the forefront of Asuka's thoughts and smolder within her. It will not help that the other pilots admire Juri and even defer to her. Utena will quietly respect Asuka's abilities but publicly denounce her demeanor, and Shinji will all but ignore her. Only Miki (and through him, Kozue), whom Asuka sees herself in, will be spared her derision and vocal outbursts. Miki, to Asuka, is a younger sibiling: a prodigy, a pilot, and a talented fencer. More precisely, she believes (falsely) that he would want someone like her in his life as a mentor, and she honestly would like to be that to him. But even he will alienated by Asuka's demeanor and she will find herself with only Juri, whose affection she will not accept (and will in fact frighten her), as her sole supporter. As a revolutionary girl, Asuka's nobility will manifest slower and less obviously than that of her peers, though arguably, it will be she who risks the most (breaking Kozue into NERV) and sacrifices the most (giving her life for Juri).
Juri has never met Takatsuki Shiori. The Second Impact prevented that from ever happening. The betrayal at Shirori's hands never occurred. When she is approached by NERV in 2013 to be a potential pilot, this highly idealistic girl immediately accepts. Her failure to synch (due to a mere few hours of her birth) and Asuka throwing it in her face leave her very bitter. She is kept on at NERV as a trainer, and later taken on by Misato as her assistant. End of the World arranges for Juri to fail expressly for the purpose of motivating her to duel. Despite this, Juri retains all of the nobility that Shiori took from her in Utena, and as such, is Utena's closest friend. We are going to play off something Ikuhara said, "There is a lot of Utena in Juri, and a lot of Juri in Utena." But unlike Utena, who wants to be a Prince, Juri is a Prince already. A wounded one, and one who still cannot express her feelings towards the one she truly loves, but nonetheless noble. I'm not certain where this is going to lead Juri, or how it will affect Utena throughout the course of the series, but it will have big impact on both Shinji and Asuka's lives. Asuka moreso than Shinji, as she will be the one who Juri's unspoken feelings yearn for, a fact that will terrify and enrage Asuka, who sees Juri only as a rival to be overcome.
The Kaoru twins were both intended to be pilots. Though End of the World sought Miki moreso than Kozue, Kozue could be molded if needed. She refuses and this drives her and Miki further apart. This leaves Miki searching for someone to be his "shining thing," and it comes in the most unlikely of forms: Ikari Shinji. Shinji, desparately needing a good friend, and Miki, looking for someone to replace Kozue, will find each other and become inseparable in the year 2014. I have this image of Miki sadly playing "The Sunlit Garden" on the piano, and someone walking in quietly, setting up a cello, and then accompanying him. He turns and looks slowly to see Shinji there, smiling. And everything just becomes perfect for them. Miki will be very hurt in Episode 1, this opens the door for Utena to come into NERV, and Shinji will have a momentary relapse before moving on. Kozue, on the other hand, will set her sights on helping Miki, even going so far as to make certain NERV never uses him as a pilot again. For most of the story, she will be a supporting character, interacting mostly with Wakaba, Asuka, and Utena, but coming into the forefront around Episode 16 or 17, when she will be the pilot of the ill-fated Evangelion Unit 03. Miki will resurface about that time, coming out of his coma. He will find that Shinji, in his absence, has grown up. While Shinji hasn't necessarily moved beyond Miki, he will have moved past his need to cling to a single person to feel important. These two characters will probably end up the most tragic in the story.
On a personal note, I wonder what Mitsuishi Kotono would think about having to play two characters (she would also play Juri) in the same anime, both of whom are main characters, and both of whom will interact with each other in some fashion in almost every episode. Misato is Juri's mentor, but more than that, she is the character that will stumble onto End of the World's duels. She will work more closely with Kaji than she did in Evangelion, and her relationship with Shinji will far more solid than it was then. This will stem mostly from Shinji's development. Her friendship with Ritsuko will suffer when she discover's Ritsuko's ties to End of the World, but she will join Ritsuko's cause once she learns what End of the World is trying to prevent. On Ritsuko's behalf, Akio will not seduce her, though he would prefer to, and thus she remains as much of a wild card as Kaji, playing two sides of a struggle but ultimately loyal to herself. I'm not certain where it will fit in, but I want to do something with Misato's aphasiac period; there is a similarity to Utena's time in a coffin there and how the two of them came of out their respective situations.
Nanami and Touga will take the place of Kaworu, who was never created, in lieu of the Kiryuu siblings. Partially, this will be to keep people guessing who the Seventeenth Angel will be (there will be two of them), and partially, it is also because it tends to fit with the Utena setting. We don't know where the Kiryuu siblings came from before their adoption, hence they could have been from anywhere, and therefore fits the mold of Kaworu's "no data exists on him." It doesn't matter what data exists on the Kiryuu's, because everything after their adoption is simply a sham to cover what happened before their adoption. Unlike Kaworu, however, the siblings will have lived a good portion of their lives among the Lilim, and have a better understanding of it than he did. Touga will be one of the supporting characters at Ohtori, very much Utena's Prince until his motivations are revealed in Episode 24. Nanami will be seen first at the Amsterdam campus of Ohtori when Kaji is investigating End of the World, and will be brought to Tokyo-3 near the conclusion of the series. She will be a test for Shinji's affection towards Wakaba.
Touga will remain as mysterious as he did in Utena, but will be seen more like he did in the Utena film. More approachable, more princelike. Nanami will show a variation of this in Shinji's company, though by that point, I think most readers will expect that from her as she will seem to be the obvious Kaworu character. Like Nanami, Touga is a test of Utena's affection for Rei. Since he and his sister are SEELE creations, they are sent to monitor Akio's loyalty. Touga will reveal to SEELE enough to let them know Akio has other plans, however, he will keep the secret of the duels to himself and his sister. Touga estimates that if he wins the power of Dios, breaking into Terminal Dogma will not be necessary, though Nanami will carry out that portion simultaneously. He will make amends with Saionji just before any of this actually happens, though he could have done so at any point before, leaving enough questions as to just how much he was manipulating Utena or if everything that occurred between them was genuine.
While it will not be obvious, this entire series is Rei's story. Everything in this series in some fashion or other revolves around Rei. She will occupy Anthy's role as the Rose Bride in the Utena portion of the narrative, created by Mikage to replace Anthy after Anthy commits suicide. Mostly Anthy, partly Yui, Rei will be more confused about her existence than she ever was in Evangelion, and this confusion with herself will preclude her from synching with either Unit 00 or Unit 01. This failure will alienate Gendo from her, and she from him. Until Utena befriends her, Rei will be completely isolated within herself, seeing the same isolation in Juri but knowing no way to relate this to her. Rei is desperately searching for an identity. When she learns of Akio and the Rose Bride, she will immediately reject him as well, not wanting to be yet another replacement (all she is, in her estimation, is a replacement). She will cling to the idea of being the Rose Bride, since she believes (with possible accuracy) that any other duplicate of her may not awaken as she did and thus it makes her unique from all the soulless Reis kept in Terminal Dogma. She will later understand that while that separates her from the duplicates, all she has done is made herself Anthy's replacement in spite of her original intentions. The complementation scene in Episode 26 will deal with Rei coming to understand that she is unique because someone loves her for who she is, regardless of her artificial origins.
Already alienated from Touga, and without the duels arranged by End of the World to give him purpose, Saionji is an easy target for Kaji. Looking for someone within Ohtori (but not on the faculty, since he cannot trust them) to be his eyes and ears, Kaji finds Saionji and brings him into the fold. Since he has always suspected Touga of knowing some dark and powerful secret, Saionji agrees. That he is part of the Ministry of the Interior's investigation of NERV is a great source of pride for him, but it will not be enough to deter him from seeking eternity once he is contacted by End of the World. He will spend a good portion of his screen time observing the NERV children and doing research, and he will ultimately and unknowingly be responsible for the events leading to Mikage's death (revealing information to Kaji) and Misato being converted to End of the World's cause. Once End of the World invites him to duel for the power of Dios, he will abandon the assignment given to him by Kaji. He will not win the one duel is he is alotted, and having lost the opportunity to find eternity (and therefore surpass Touga) will spend the remainder of the series in despair.
The question I got asked most when I initially proposed this story was "Will being around Utena change Shinji?" Yes, though it will be four Utena characters (Miki, Wakaba, Utena and Juri) that will eventually allow him to move past his hang-up with Gendo and move on. I don't want Shinji to remain as he did in Evangelion; I want to see him grow up and become something new. While this is going to remove a good deal of angst from the latter half of the series, enough will be going on with Asuka/Juri and Rei/Utena that having Shinji continue to be a wreck would make it overkill. Unless the discovery of Rei being created from Yui is needed to make Shinji duel, I don't think it will come up; Rei is meant to really be Utena's conundrum and he's going to have his hands full as it is simply having a girlfriend. Rei's failure to synch will bring Shinji into NERV one year earlier than he arrived in Evangelion, thus when he see him for the first time he will already be a trained pilot, have a very healthy relationship with Misato, and a strong friendship with Miki. He will be more confident in combat and more noble in his purpose (even more so as his relationship with Wakaba grows).
Utena will be much the same character she was in Utena. She will have a very close friend, a very large circle of friends, and the dogged determination needed to get Rei to open up to you. She will be as na´ve and innocent as before, but this will be tempered somewhat by the violence that an Evangelion pilot must commit. Of the three main pilots, she is the one who believes the most in what she is doing, and the one who will do it for entirely altruistic reasons. One of the key differences will be that unlike Anthy, Rei will not manipulate Utena. She will instead silently endure her discontent, never fully understanding why Utena insists on protecting her. Rei will want Utena to be the One Engaged but only because it will validate Rei's existence. Utena will have no clue just how much Rei wants to be the Rose Bride, something that all the other Duelists will at least suspect even if they don't know Rei's motivation. Because Akio cannot reveal himself to the pilots without arousing suspicion, she will not meet him and will not be seduced by him, something that prevents her from becoming "more feminine," as she did during the final arc of Utena.
Wakaba is not an idiot. Half of her fascination with Saionji in Utena was the belief that if she got him, her own status would be elevated and she could become one of the "special people." Seeing Shinji, she will instead set her sights on him, as he is a much more attainable target and the prestige involved in being the girlfriend of an Evangelion pilot will be just as great or greater than the prestige of being the girlfriend of an attractive member of the Student Council. He will fall in love with her easily, something she will not expect, and will fall quite in love with him as a result. The two of them will, I think, complement each other well: Shinji will get what he needs (and wants) from her, and she will get what she wants (and needs) from him.