I think the reason of Mari Illustrious Makinami's huge breasts is that she'd had a baby (SS Asuka-original - "SS"="the Saal-Schutz" (Hall (Super/Elite) Security Guard) ) when her own Mari's original clone had been made by her and her German husband. During and/or after female's pregnancy, her breasts get larger, more sensitive than ever before. I think Kyoko -Kyoko Zeppelin Soryu was a one of the first Mari's clones for her EVA Unit-02 project -for deceiving the NERV. Über ihre eigentliche Persönlichkeit ist "wenig bis nichts bekannt"-Klon. Man sollte annehmen,dass sie über großes Wissen besitzt, da sie Wissenschaftlerin und Mitverantwortliche für den Bau der EVA Einheit 02 war. Nach ihrem Unfall, einem Kontakt Experiment mit dieser Einheit, verlor sie ihren Verstand, doch blieb der Mütterliche Teil ihrer Seele im EVA. Mari allerdings ist kein Klon aus Mari Makinami alleine (+ Mari's klon Kyoko Zeppelin-Asuka's fake mom to deceive NERV).
This story has been started by Yui who happened to know the evil power will be overwriting the current universe. Then she started her goddess project using her slave ark angels (Gendo/Mari/Asuka/Rei) all of them was tied by glasses, chokers or red hair ties. To complete this mission (project) she needed her son the savior Shinji and the most powerful warrior, genius and all-mighty angel "Mari". The last scene of this movie, nobody puts on Her "slavery symbol" of chokers ,glasses or red hair ties ... except Mari who has been given the last arkangel's mission owned to make Shinji happy ever after. Goddess's last slave-gift for Her Son, the most perfect "almighty" (beautful/guardian/highest IQ owned) female and/or spouse in the world " Mari" .