Nia follows along eventually and proceeds to call Shinji, Shinja. Even after the mispronouncement is pointed out to her, Nia still continues to use it on habit throughout the story.
The second half of the third Parallel Works, which details how Nia met the Dai-Gurren Brigade in this universe. And as an added moment of heartwarming, Kamina is still alive when it happens.
Not only that, but Nia escaped with the help of Viral
The growing bond of the Rangers throughout the entire story is very endearing.
The Mexican Standoff in Chapter 19 is a direct result of Misato calling Shinji a coward for not going back to Nerv. Roger, Van, Bit, Heero and Kamina took clear offense. As the damage to Misato's room clearly demonstrated.
The budding romance between Shinji and Hikari is extremely awkward for both characters(Especially with no thanks to their teasing peers), but it's a genuine chance for happiness that the Eva Pilot becomes more and more willing to take. Hikari cements their relationship with a Big Damn Kiss in Chapter 24
Roger's interactions with his daughter and even Dorothy, his wife.
Shiro standing up for Noriko after she's discovered to be a cyborg in Chapter 25.
The sisterly bond that the Love Interests of the rangers share with each other. Especially when the older ones encourage and look out for the younger girls.
In particular is Hitomi who has experience as an older sister herself.
Believe it or not, Kaiba still clearly cares about Mokuba despite outward appearances. Look no further than this exchange in Chap. 25 when Mokuba initially thinks that Seto is dead.
"Is my little brother crying? I thought you wanted to run my company?"
"After I win it from you fair and square big brother!"
With the understandable exception of Hikari, Hitomi and the rest of the girls actually welcome Euphemia with somewhat open arms. Leena let's Euphie borrow her clothes, Annie talks with her about ponies, Nia and Euphie confide in each other about their fathers, and Hitomi even decides to determine Euphie's true nature.
Keep in mind that this is after they're told that Euphie is the massacre princess for a reason.
Kaji and Duo sticking up for Misato when she's initially barred from helping Noriko find a now-missing Hikari
While still a bitch, it's nice to see that Asuka truly respects and admires Nunnully despite the princess' handicaps