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Shinji accepts the human instrumentality project in the show and he rejects it in the movie. that also leads to the theory that the rebuilds are sequels to Eoe, when they say "rebuilds" it's a literal term the world of eva in these new films is a rebuilt earth that's why there are similarities to the show but also new twists
the 1st film gives a few clues
they show the moon having what appears to be a huge blood stain/ perhaps lcl stain on the surfaces this would match perfectly to what happened when angel Rei bled all over the moon in eoe. Secondly when Kaoru shows up in the last scene with what appear to be 5 coffins next to him:"This time I'll definitely make you happy shinji" again at this point in the movie series they haven't met so I think this is a fairly strong clue as to what's going on and here again this follows with the idea that this is a do over.
the second has a few more call backs like shiji trying to destroy the geofront by stomping on it (in eoe this was in his mind he was boy stomping on it) in the film he does it in eva unit 01 that's fairly minor but something that does stick out.I think the most telling sign in the 2nd film is Seele's logo it's changed slightly ..what did they add? a serpent biting it's tail..that's ouroboros a symbol of something reaping infinitely. Obviously this is all speculation but it's fairly interesting to talk about
I haven't seen the new movies, I thought they were doing the school comedy into full extent, or I read it somewhere, I don't know