Cowardly Lion: Even more so than canon, considering the inherently, mind-scramblingly terrifying nature of ENEs.
Dream Sequence: Shinji has a weird one at the start of chapter 4.
Eye Scream: When Asherah ripped out one of Unit 01's eyes, Shinji's synch rate was high enough to experience some of the pain (although not enough for any physical injury).
Has Two Mommies: Shinji was raised by two women (a FSB agent and an Ashcroft sorceress) selected by his father.
I Don't Know Mortal Kombat: A non-video game variant, where Shinji's skills are strictly attuned to being in the Eva, so he can do nothing but be a punching bag for Toja while in school. His gun training does transfer to the Light Gun Arcade game, but those are designed for scouting potential military recruits anyway.
Only Sane Man: Shinji sees himself as this, what with his constant complaining and lampshading about the ridiculous circumstances in his life. It's not entirely accurate.
Naked First Impression: When Shinji meets her for the "first" time, when she is naked in the medical tank and missing one eye. The real (maybe) first time is when she incinerates some hostile operatives Alma-style right before his eyes, which causes Shinji to feel very uneasy everytime he is near her.
And, naturally, the first time he actually talks to her is the same Naked First Impression as canon.
No Social Skills: Slightly subverted, as AEE!Gendo didn't dare to neglect Rei like he did in NGE. However, her White nature means that his efforts were mitigated, and she's still cold and distant.
People Jars: Rei in the medical tank. Wait a moment. A precognitive in a tank filled with orange fluid? Sounds familiar.
Ace Pilot: According to Ritsuko, she was one of the best pilots of her generation.
Christmas Cake: Emphasized in Chapter 8 when Toja and Kensuke call her Mrs. Ikari.
Cloudcuckoolander: Shinji sees Misato as this when they're off duty. Ritsuko ties together an explanation for this and her being a Lethal Chef (see the latter's entry below).
Drives Like Crazy: As usual, now with her car's interior upgraded with stuff that is better suited for aircraft. (It's a flying car, but still...)
Lethal Chef: She has the same sensory issues (and resulting culinary fallout) that she had in ANE. This time around, though, it's due to brain damage caused by exposure to the environment of Leng as opposed to ANE's more directly brutal reason. At least, that's what Ritsuko tells Shinji. It's only part of the truth, and the rest, from her inner dialogue, is best left unspoken.
Tuck and Cover: She did this to Shinji when the nuke was used against Asherah.