P3 = NGE

How Persona 3 Is Literally Neon Genesis Evangelion: The Videogame
An Autistic Thesis by Anonymous

1. Plot
The basic plot outlines of P3 and NGE share a surprising number of elements. In both stories, an organization which goes by an all-caps four-letter word is the central figure in the efforts to take down a limited number of incredibly powerful monsters. Both organizations, SEES and NERV, have as their frontline soldiers young teenagers who access a power that, for various reasons, only they are able to use. This power has a significant bond to the teen, and is unique to them, though a particular “blank slate” character has the ability to access forms of the power- MC's “Fool Arcana” and Rei's ability to pilot Unit-01.
The organization, however, is headed by a man who does not, in fact, seek to SAVE the world by killing these beasts (Full Moon Shadows, Angels), but rather bring about its prophesied end. This older man has the rest of the organization believing that they are doing good, and near his endgame, uses his influence over a demi-human short-haired semi-emotionless character to help bring about his plan (Ikutsuki's remote control of Aigis, Gendo's manipulation of Rei).
As it so happens, the prophesied end DOES come about, and an attractive young man approaches the main character (Ryoji here being the Kaworu to MC's Shinji) to provide him a choice- though this choice does not actually affect the outcome. This young man turns out to be the final of the monsters to be slain.
As the story draws to a close, the great force which sought the end of all humanity pacified (Nyx, GNR/Lilith), the main character ends the story in close proximity to a young woman with whom he shared a close bond, and who was introduced about ¼ of the way through the story (Aigis, Asuka).

2. Characters
While very few of the P3 characters can be said to be DIRECT corollaries to Evangelion characters, several of them have traits that seem like a “mix-and-match” of various Eva characters.
Ryoji and Kaworu, as detailed before, are the closest match between the two stories.
Yukari shares several backstory elements with Misato Katsuragi, as both had a scientist father who died and for whose sake they join their respective organizations, only to find that said father was at least partially responsible for the unleashing of the monsters they face. Both also witness the death of their fathers at some point. Their personalities, obviously, could not be more different, with Yukari at the most having a vague connection to Asuka.
Aigis, the vaguely emotionless demi-human created for the purpose of fighting the monsters, is a very close corollary to Rei, but also takes Asuka's place at the main character's side in the end of the story.
Shinjirou serves as an iffy Touji corollary as a very physically tough young man who dies in action, with a young boy blaming himself for the death.

3. Themes
Evangelion's primary theme was communication between others- specifically, how painful it could be, and how worth it it could be despite that. Persona 3's Social Link (or, in the Japanese, Commu) system is not dissimilar from that. It's notable that P3's S. Links are substantially easier to Reverse than P4's. Socializing is actually somewhat risky in Persona 3, as a wrong choice can turn your level 8 S. Link that you get tons of bonus XP from into a flat nothing. But you must do it regardless in order to reap the rewards.
Themes of death and echoes of mythology occur throughout both stories as well, though P3 centers on Greco-Roman mythology and NGE takes on a Judeo-Christian theme. P3 even begins to echo the Judeo-Christian theme near its end, however, with MC's ultimate Persona Messiah and the obvious Christ symbolism of him giving his life to form the Great Seal.
Both stories are surprisingly dark, though not in a campy , tryhard way. Rather, they naturally feel dark, and the stakes feel very real. The deaths of neither Touji nor Shinjirou come out of left field- the atmosphere as it had been presented in each story up to that point very definitely felt like death could occur at some point.

As a final note, Persona 4, the brighter, fancier, unendingly milked, and thrice as shallow followup, would be Persona's “Rebuild” series.

And both Aigis and Rei are best girl.