The popular theory came about during the Rebuild films
During the celebrations for the 1st anniversary of Evangelion 3.0+1.0: Thrice Upon a Time's theatrical release last night, director Hideaki Anno and Amazon Prime, the service streaming the film around the world, teamed up for a live stream where the creator answered fan questions. Many of those answers were transcribed onto Twitter by Studio Khara, giving insight into the film and the production around the popular franchise.
One of the questions asked by fans is if Anno's wife, Sugar, Sugar Rune manga creator Moyoco Anno, was the inspiration behind Mari. The theory is popular in Evangelion fan communities as fans interpreted Mari saving Shinji in the new films as a reflection of Moyoco saving Anno from his depression through her love for him. As in the past, Anno has directly denied the similarity between his wife and Mari, stating "this [theory] merely only the assumption and speculation of a handful of people."
Here's a translated full answer to the question (which was broken up over multiple Tweets):
"We have seen various articles, videos, etc. that claim Mari was modeled after Anno's wife, but this merely only the assumption and speculation of a handful of people.
At the time of production, this would have been impossible. Mari's personality (as well as Asuka and others) was created by director Tsurumaki's hand [rather than Anno].
It's a bit of fun for the audience to interpret characters and storylines as they wish, and [Evangelion 3.0 + 1.0] is a playground of intellectual fan speculation.
That being said, it is sad to see the staff and their families disparaged by baseless assumptions, so we will clearly deny that this is the case."
This isn't the first time the rumor has been denied, with Moyoco Anno coming out against the rumor asking people to research her life before comparing it to a fictional character. Tsurumaki has also spoken about his development of Mari in interviews, explaining that she "is a touch detached from the seriousness of Eva, which I think is what makes her seem more FLCL-like."
When asked later what Anno thought of facts spread by people who are not involved with the production becoming "fact," Anno just replied, "I think it's annoying."
Evangelion 3.0+1.0: Thrice Upon a Time was released in Japanese theaters on March 8, 2021, finally coming internationally via Amazon Prime Video on August 13 of the same year. It is currently the 10th highest-grossing anime film of all time in Japan and the 36th highest-grossing overall in its home country.
Source: Studio Khara on Twitter
Daryl Harding is a Japan Correspondent for Crunchyroll News. He also runs a YouTube channel about Japan stuff called TheDoctorDazza, tweets at @DoctorDazza, and posts photos of his travels on Instagram.