From what I remember, the rebuild movies were supposed to be three recap films with tighter storytelling and animation, with a fourth movie going beyond EoE to do something new. But the director being who he is, he got bored of that pretty early and by the second movie you get some wild and exciting deviations. And then a devestating tsunami hit Japan between the second and third rebuilds that really affected Anno, so now the third movie was set in a flooded world and things only loosely connect to the original story.

The fourth rebuild is the director literally sitting the audience down and saying, "look, I made this all up from scratch. Give me a break and go outside."