I admire some things about the manga canon, but when it comes to the ending, it's just as messed up as the End of Evangelion ending.
I mean, here are some of the things I found wrong with its outcome:
1) They just killed off Toji Suzuhara, and never speak of him again. 2) It seems that those killed before Instrumentality aren't entitled to a rebirth, like Misato and Kaji. 3) Shinji still seems separated from his parents, and there's no mention of them in the aftermath. 4) There's no mention of any of the other characters aside from Shinji, Kensuke and Asuka. 5) Where's Rei/Lilith?