The first half of the movie made sense, and was infinitely better than the original ending of the series. It suffered from "the author never really had a plan for an ending".
Personally, I would have ended it as everything returning to normal with the Government having had the troops kill everyone at NERV and then "covering up" the whole saga. They could say that it was a criminal conspiracy with Gendo faking everything to steal money for personal gain, and they could install the government spy Kaji as the "hero who uncovered the plot" before Gendo had him murdered.
You can get fan theories about all of the questions you have about Rei and so forth (she's a clone of Gendo's wife after Gendo's wife died/transcended the next evolution of humans/God-like state via contact with the Evas), but I think fans have thought it through infinitely more than the authors did. I guess they just couldn't dig themselves out of the plot hole they dug. They probably thought it'd just be a 26 episode monster of the week show when they started.
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