... I have doubts about such censorship stories. I expect it had more to do with Anno realizing by the midpoint of production that the characters he’d created couldn’t bring the story to the end he originally had in mind.

What do you think were the original goals/end of Eva, and how did Anno mess up?

To paraphrase Anno’s own words, he wanted his characters to start from a damaged place and change, presumably maturing and becoming better, more self-sufficient human beings through their struggles and interactions with each other. But he created characters that were too damaged and insular for that to happen in any believable manner. And instead of getting better, they got more screwed up as things went on.

...

I spoke with people working as closely as anyone with Anno during the latter part of the production and broadcast in particular, and they volunteered the information that Anno was just trying to find some way of putting a smile on Shinji’s face by the end of the series, after he was brought to the hard realization around Episodes 12–13 that the characters he’d created weren’t capable of whatever positive change and outcome he originally envisioned. I think the break is first made explicit with Gendo’s remark out of nowhere around that point to the effect that the ultimate end of evolution is self-destruction.

...

This is what I was able to pick up in conversations and scuttlebutt around the office at the time. Anno had been trying against reality during the first part of production to bring things around to his original intended vision. By the midpoint of the series, he finally gave up; note the changes in the avowed purpose of the Human Instrumentality Project, for example. He up-ended the whole thing in the last two episodes of the TV series.

So, if this is true, it means Anno originally wanted to give a happier or at least a more hopeful ending, but (both real and fictional world) reality thwarted it...