Kaworu's Establishing Character Moment. He's ambushed by a trio of upperclassmen after he stopped them from bullying a younger boy. Toji is about to step in when Kaworu just wipes the blood off his mouth and simply says "I got this." Then he proceeds to thoroughly wreck the bullies in a matter of seconds, using his superior streetfighting skills.
Whenever it comes to piloting an Eva, Rei got a massive increase in competence from canon. Starting with soloing Sachiel via aerial acrobatics and evasion stances straight out of TheMatrix.
She could not contribute much to the Shamshel battle - but more than made up for it against Ramiel by first evading its Attack Drone assaults despite being restricted to the ground, then taking out said attack drones - then dropping onto Ramiel from orbit and plowing into the Angel with an Inazuma Kick. And if that wasn't enough, she then knifes Ramiel in the core and does an Unflinching Walk before remotely detonating the knife's built-in explosive charge with a fingersnap.
Speaking of Shamshel, she gets her own moment when she successfully manages to trap Kaworu and lectures him for not paying attention, throwing his earlier taunt right back at him.
The AEL as a whole deserves credit as well for designing and building the Evas without SEELE ever finding out.