Many people got this impression that Gainax is just treating the Evangelion series as an awesome cash cow, since the Rebuild, with largely similar storyline for the first installment of the 4-film series (as compared to the original anime), had earned them considerable amount of money.

Cosmetic changes aside, there are indeed several aspects of the new storyline that might signify a change in how things turn out for the next few films – like how they’ve axed a few angels out of the series, the puzzling change of Lilith’s face, the change in the SEELE and NERV logos and etc. Indeed, it’s suspicious when the animators took great pain to faithfully recreate many of the insignificant minute details (like the passengers on the train, the clutter on Misato’s apartment).

I can’t help but speculate too!

The changes that are beyond cosmetic are likely very intentional, given the chalk-outline opening scene. Making the water red in pretty much all scenes, for example, and moving Lilith’s mask from her to the Seele monoliths. Also strange things I don’t get, like the track number and time change of Shinji’s music player. Only the seconds remain the same number. When everything is so faithfully re-rendered, a change like this is suspicious.

While I don’t know because I haven’t seen the rest, could this be the result of Shinji’s wish…? A chance to try again? It’s my speculations :p

episode one — Sachiel’s leap
episode two — Gendo’s meeting with Seele members

The images are there, they’re just not linked correctly.