There’s some great stuff in here – I love the Handler/Commander being player roles rather than NPCs. Your system of Pilots going off-mission, Handlers aborting, and Commanders revealing secret objectives is fascinating (I forgot how much mistrustful and secretive adult-kid dynamics drove Evangelion’s character drama)!
Would love to one day see a version with less text-heavy layout or with your examples laid out in a template mission. You might like SAD TEEN MECHA PILOTS as another directly Evangelion-inspired ttrpg!