Ass Pull: An enormous spaceship capable of carrying five Evas to Planet DELTA (which orbits the Sun opposite the Earth) in a few days is thrown together in a few chapters. It even seemingly has artificial gravity, despite this not existing in Evangelion.
Ensemble Dark Horse: John's brother Charles is introduced as a simple computer programmer, but proves to be quite the commando when SEELE attacks. He also seems to have the ability to take a four month holiday from his job with no repercussions. As noted by the MSTers, Charles is more useful than John.
Charles also managed to clone himself in one episode.
Idiot Plot: Jeff Garynn's method of assassinating someone? Attack them in broad daylight in the middle of the street, shout "NO WITNESSES" and then start by gunning down the innocent bystanders.
On a broader scale, this may cover the entire fanfic.
Moment of Awesome: the final battle against Justice in chapter 12 actually approaches something resembling exciting and dramatic action, ditching a lot of the hallmarks of the goofy CurbStomp Battles that mark the rest of the fic. Of course, any drama is quickly lost via Moment Killer in a flood of Techno Babble (at the end of chapter 12) and Glurge (most of chapter 13).