- Better Than Canon: Although the quest strictly adheres to much of the lore and themes of the show as well as being faithful in representation of the characters, the more optimistic tone, character development, and an open-ended but hopeful Bitter Sweet Ending make a strong case for a more enjoyable experience than the original show or Rebuild.
- Moral Event Horizon: Gendo crosses this when he holds the world hostage by resurrecting Adam and attempting to force Rei to start Third Impact to save her loved ones from dying.
- SEELE manipulates the U.N. into authorizing an attack on NERV, leading to Tokyo-3 and all its innocent inhabitants (including friends of the pilots) dying.
- The Woobie: The T-RIDEN-T crew gets a pretty raw deal throughout the story, being Locked Out of the Loop on the conspiracy behind the scenes as well as acting as mere support for the Evangelions. Their JSDF base and any friends they may've had are lost when SEELE attacks NERV.
YMMV / The Shinji Ikari Raising Project