Gendou's fanboying over Shinji seems to parody the daughter complex in comedy mangas, and no one wants to remember this element of his original characterization in the context of a high school comedy (also, it offers a scary new explanation for why he thought in The End of Evangelion that he'd be a danger to Shinji if he raised him. The jokes about Shinji being a mama's boy. Ritsuko's occupation as the school nurse, when you consider that she acted as the school director with Touji in the original series and manga. This manga also sheds light on Naoko Akagi's special brand of mental illness, Ritsuko's obsession with the Ikaris and Kyouko's lack of parenting skills. Thank you, Raising Project.)
There's also the possibility that Yui participated in creating Rei.
On a lighter note, how does Gendou know how it feels to wear the shiny girly swimming suits?
Gendou's attention-seeking/inspirational speeches about masculinity -and the fact he fails to ever impress anybody for a whole page. Same for his grand demonstrations of affection towards Shinji, which look more like Godzilla attacks than anything human◊.
The ohanami scene, where Kyouko starts pestering Asuka about her relationship with Shinji and how she'd really like to see their kids, and everybody facefaults and goes Super-Deformed.
Asuka's clumsy fights with Kaworu over Shinji, and the scene where she calls him a homo and he shrugs in absolute disdain. Yui in a baseball outfit, especially since she is in command all the time and was spared the fitness bike silliness.
Heartwarming Moments: Many of Shinji and Rei's interactions with Yui. The scene where Shinji is sick in bed and tended to by Rei; his reciprocation when she gets sick in a recent chapter. Shinji's multiple rescues of Rei in virtual realities during synchro tests. Shinji's moments with Asuka usually involve a scene on the beach and a reminiscence from their childhood but are generally followed by an Accidental Pervert + Megaton Punch incident. The scene where she eventually kisses Shinji was very fluffy, though. (When Shinji compliments part of Asuka's bento lunch, he thinks he offended her by not praising it enough, but when she walks away we see that she's SO HAPPY that he liked some of it!◊) Most of the ohanami episode, with the (short-lived feel-good "happy families" feel. Asuka's few encounters with Kyouko involve a rain of adorableness. Gendou's daydream about a grown-up scientist Shinji both qualifies as a Heartwarming Moment and as a Funny Moment. And let's face it, Yui embracing Gendou publicly (without Tanging him!) after his rescue of the MAGI system was surprisingly cute.
Asuka/Rei. While things between them are platonic and only Shinji has their romantic interest, they do get subjected to Homoerotic Subtext throughout the series. For example, there are many of Shinji's dreams and title illustrations. Next, they become even more friendly toward each other late in the series. Then, in one extra chapter they have a nearly full blown yuri scene when Rei gets intoxicated by alcoholic odor, granted this is only played for fanservice. Finally, both girls get cast in the leading roles of Romeo and Juliet and immediately following that, a mishap leads to them having an Accidental Kiss with each other.
Moe: The manga is like an inventory of Moe stereotypes and more; Shinji is just adorable.
Moment of Awesome: Whenever the situation looks hopeless, Gendou temporarily becomes incredibly competent and Kamina-level badass for a few pages and a Funny Moment occurs. Shinji also saves the day a few times, but not as spectacularly.
No Yay: Gendou-Naoko. It's kind of like Shinji-Misato with wrinkles and an intolerable amount of deviousness.
Rescued from the Scrappy Heap - Gendo. To clarify, he's never been a scrappy in this series, but many fans didn't like him much. However, this series may as well be titled Neon Genesis: The Gendo Ikari Popularity Project for how much fans love this version of Gendo.
They Changed It, Now It Sucks!: One of the possible reactions to this... if you presuppose Raising Project has anything in common with the original series!
This Is Your Premise on Drugs: Strange and unrelated things are being made at the Centre for Artificial Evolution, such as Moe swimsuits and probably "special vitamins." What do you think Gendou derives his energy from? From Moe swimsuits and fitness bikes.
The Woobie: Rei is particularly fragile emotionally and seems to have gone through a lot of isolation.
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