Top-down close-up of Shinji;
His words sound anxious.
SHINJI:“I’ve never practiced anything like that before.”
NemZ: Um... Isn't this EXACTLY what he was trained to do? We don't see him getting a hand-to-hand instructor (seriously, why not?) but centering the target is definately something he can do.
thewayneiac: I doubt if he has to compensate for all that with the palette gun.
Kendrix: Here, in this precise Moment, we're still dealing with Prologue Arc Shinji who has no clue what he is doing in Tokyo 3, and therefore clings to his training for guidance. Okay, Shinji never really stops clinging to others for guidance, but he improves GREATLY after this battle - He demonstrates much more of a will of his own in the subsequent episodes/his interactions with Misato and Asuka.