Back in the early 2000s, Anno was working on-and-off on some vague and tentative plans of one day putting together some sort of epilogue story to the original Evangelion TV-series. The project would instead eventually evolve into Rebuild.
The film series was originally conceived as a direct adaptation of the original television series with updated visuals, a few key changes, and a new ending. However, 2.0 and beyond ultimately established that the creators wanted to go in an entirely different direction altogether.
Rei was initially supposed to die during the battle with Zeruel in the second movie, but screenwriter Yoji Enokido argued that she should survive this time around. However, one of the directors, who really wanted to develop the third Rei, was pissed off at this and managed to overturn the decision in the third movie, where it's revealed that Rei wasn't rescued after all and now Rei III has replaced her. Then it turned out Enokido had the last laugh after all, as the final movie overturned this decision when it revealed Rei's soul actually was still alive trapped in Unit-01, and Shinji successfully saves her at the end of the story.
Because Mari's character wasn't finalized by the time she made her full appearance in the second movie, a number of concepts for her were left on the cutting room floor. To wit:
It was originally planned that Mari would be The Rival to Asuka, eventually surpassing her and presumably playing a role in her character development. This plot thread, and whatever was intended for it, was soon abandoned in favor of making them close teammates.
Another concept for Mari that was dumped had her owning several cats at home, and she would have had tattoos of them on her body. Her cat-eared helmet and her habit of punctuating her sentences with meows may be relics of this idea.
There were plans for Mari to basically take over Asuka's role from the original series, including giving Shinji his first kiss.
2.0: You Can (Not) Advance
According to Anno in the Complete Records artbook, the script changed around forty times throughout production.
The Third Angel underwent several minor changes in production, with Anno himself creating the concept before handing it to Mohiro Kitoh. At one point, they jokingly discussed giving the skeletal angel the ability to somehow emit corrosive liquid from its mouth.
A scrapped plan would've had Asuka and Mari piloting Eva Unit 02 together during the battle with Zeruel. In the final film Mari pilots it by herself since Asuka is hospitalized, though storyboards of the original idea can be seen on the DVD extras.
Another abandoned idea, which went as far as the storyboard stage◊ and is included on the DVD release, would've shown Bardiel's mental attack on Asuka in greater detail. At one point Asuka would hallucinate her own face being peeled off, and to get worse, the face would stare back at Asuka and begin mocking her. That last part ended up reused in 3.0 + 1.0.
Earlier versions of the same scene would have included hallucinations featuring Kyoko, implying Asuka's backstory in Rebuild remained vaguely similar to that in the original anime. This was disposed of for good in the fourth movie, which reveals Asuka is actually a clone from the Shikinami line, this means her backstory was changed at some point (her flashbacks revealing her past don't imply she knew or cared about her originator).
In earlier scripts, Asuka would have participated in the initial Zeruel battle as in the television series, albeit still injured from the Unit-03 fiasco.
3.0: You Can (Not) Redo
Almost nothing of the preview for Rebuild 3.0 made it into the actual film. Anno revealed in a stage greeting that the movie was initially supposed to follow the events just after 2.0, as seen in the preview: Gendo and Fuyutsuki would've been stripped of their leadership positions at NERV and went on the run as fugitives until Gendo returned, took back control of NERV and used the Mark.06 to restart Third Impact, at which point most of NERV split off to form WILLE and Kaji pulled a Heroic Sacrifice to abort Third Impact, with the last movie would had picked up after the timeskip. However, Anno didn't like the idea to have a movie without Shinji, so he skipped the story to Shinji's awakening 14 years later.
Funimation originally planned to release You Can (Not) Redo on home video in 2014. However, Funimation worked directly with Khara to re-translate and re-record the film from the beginning, reportedly due to the negative audience reception of the theatrical release. Thus, it was delayed until 2016.
3.0+1.0: Thrice Upon a Time
It was originally going to be released in 2013. However, it became stuck in Development Hell for quite a few years due to Anno's Creator Breakdown and his work on the 2016 Shin Godzilla movie. And then 2020 came around...
Evangelion Unit-8+2 that was shown in the preview at the end of 3.0 is never part of the movie proper. The closest we get is a brief moment where half of Unit-08 is covered in blood, making it the half red/half pink that was in the trailer.
Amanda Winn-Lee, who voiced Rei Ayanami in every incarnation of Evangelion up to that point, was offered to reprise her role for the original Funimation dub of the first Rebuild film. However, since she had to care for her son Nicholas at the time, she turned the offer down and was replaced by Brina Palencia. Winn-Lee eventually reprised her role when Amazon redubbed the previous three films on top of the fourth.
When Amazon bought the rights to re-dub the Rebuild films, the studio asked ADR Director Joe Fria if he could use a new cast or bring back the original voice actors. He chose the latter because, while he respected the Netflix redub of the original series, he noted the negative fan reception it received over not bringing back the original English cast.
◊ and is included on the DVD release, would've shown Bardiel's mental attack on Asuka in greater detail. At one point Asuka would hallucinate her own face being peeled off, and to get worse, the face would stare back at Asuka and begin mocking her. That last part ended up reused in 3.0 + 1.0.
