>>4082939One thing must being specified. Asuka, Misato and Ritsuko didn't had an instrumentality experience, they died before the beginning of the Third Impact. Many people thinks that Shinji and these other characters had a collective instrumentality, but it isn't so; instrumentality is a personal experience, it's either you having a vision of your inner hopes and desires, or facing your nightmares, like for Shigeru Aoba* and ultimately Shinji. The people who Shinji sees in his instrumentality are projections of his insecurity and diffidence, people who in the end he admits that never considered as friendly, because for him their affection was a farce to use him in some ways. He doesn't see Kaworu because he loves him, and they reconciliated in the very moment he asked Shinji to kill him.
What Shinji realizes in his own instrumentality is that he will no more condiscendent with those who he doesn't trust, so, when he wokes on the beach near to Asuka, who was likely resurrected and put next to him by Rei/Lilith, he suddenly relives the vision he had, and has the instinct to kill her, but he desist because in that situation, in a dead world, any action would have been meaningless.
*The canon description of Aoba is that he's a nihilist; in short, nihilists believe that nothing has value, or that this value is marginal and transitory, they're amoral, practical and materialists. Aoba most likely had no affections, dreams or hopes, and when he experimented his instrumentality he faced the emptyness of his ego, that took the form of a mob of Rei clones, who, like avenging ghosts, came to him to drag him into the darkness, and he was compresibly scared to hell about it.