>>3549703Shinji is the same as NGE because his name is written in the Book of Life I think. It's not that they didn't love each other, it's that circumstances make them outgrow them because they were repeating a cycle of hurt. If you watch 3.0 again, Kaworu was both content with things being "unchanged" but at the same time he was encouraging Shinji to change, so he was also wishing for this to finally end in a good note. He tells him before exploding that "The self can be transformed" ("don't be afraid of changing"). When he sees Shinji has finally changed, he spills tears of JOY.
I think what changed is that Shinji was no longer the only person he liked as individual and shit. He tells Kaji in Instrumentalty his gratitude because he saved him too. We have a shot in 3.0 of Kaworu standing on Kaji's old watermelon field as a called out of Kaji, so he was probably grieving his loss. He loved Shinji but he also realized he can care about other people.