This is a post that I tried to make twice but for some reason reddit mods are censoring it, so read it as a reddit post and discuss:
First and foremost, I'd like to make clear that I just really, really love Mari. I do get that there are people that don't like her and they have their reasons, but for reasons I won't bother explaining in this post I really like her
Mari keeps pushing Asuka about Shinji
For now, let's ignore the whole thing about whether Asuka and Shinji are over their crush or whatever, since it's not the point. Instead, let's focus on how Mari blatantly tries to push Asuka to either admit or to act on her feelings towards Shinji(https://evangelion.fandom.com/wiki/Mari ... te_note-12). There are several instances in which Mari tries to make Asuka deal with her unresolved feelings towards him, not only during the movies but, based on the canon 3.0 prequel material(https://imgur.com/gallery/sJTaCe2) - that apparently a lot of people are either not aware it exists or simply mistake it for the explicitly not canon Sadamoto manga - she's been doing that for at least some time. For all matters and purposes, she spends a great amount of time and effort to push those two back together, or at the very least to make amends. Now, not only that amount of insistence doesn't sound like a very logical thing to do if she's interested in Shinji herself, but it's also worth noticing that:
Mari never shows any kind of romantic interest on Shinji
Now, even though how the characters portray their feelings is a major point in the whole franchise, Mari never shows any kind of explicit or obvious romantic interest on Shinji. While not doing so wouldn't necessarily mean much to a character like Rei, Mari's personality is shown as being blatantly honest and carefree, making an eventual romantic interest being much more likely to be expressed in less ambiguous terms - like telling Shinji she likes him/loves him
The movies are supposed to be open ended, especially the last one
Think about it(https://i.redd.it/s4b8skmmi1y61.jpg), not only the movie is supposed to be open ended, but also the entire idea behind the new theatrical releases. Even though many people interpret Anno allegedly pairing Shinji with Mari as a big fuck you to everyone that wanted or expected him to end up with either Rei or Asuka, that notion is mostly due to the general idea some people have that he hates the fandom or deliberately makes choices to piss people off. Now, I won't get into the merit of that notion, but let's just say that it makes much more sense to simply not pair Shinji with anyone specifically. Why is that? Because it simply is the best possible choice. At the same time he doesn't alienate a huge part of the community by picking one over the other - even though he could since he's already claimed that his favorite is Asuka - he also allows the viewer to reach his own conclusions. Not pairing Shinji with anyone means that everyone can pair Shinji with anyone - fulfilling the open ended premise that the whole franchise has.
Their dialogue is widely misinterpreted
Regardless of how open ended the general premise is, some things can be inferred with a certain degree of certainty. One of those things is the whole idea behind their dialogue at the end of the last movie. While some people saw that as some kind of romantic exchange, we need to take into consideration all of the mentioned above and, especially, Mari's personality. Not only she smelling him is a direct callback to when they first met, but her behavior is on par with her previous behavior throughout the movies - she doesn't act any more romantic or invested into him as she normally did. His response isn't given in a necessarily romantic manner - instead, it's given in a way to highlight his maturity and growth as a person(https://evangelion.fandom.com/wiki/Mari ... te_note-14), explicitly demonstrated by Mari's surprise at the fact he answered her in a very confident manner and he mentioned her huge milkies(https://static.wikia.nocookie.net/evang ... 0421150349), two things the usual Shinji normally wouldn't have done.
The assumption they were allegedly paired based on some people's interpretation of Mari as Anno's wife is flawed
While the whole idea of pairing Shinji with either Rei or Asuka would represent the bind to the past or the status quo and with Mari representing the new or the future that's still to come is a rather seductive theory, in the end it meets a major problem: an inspiration doesn't mean an expy. Some people have taken the idea that Mari has been created based on Hideaki Anno's wife and used to justify Mari and Shinji allegedly ending up together, since Shinji is supposed to be Anno's expy. The thing is, he claimed himself that everyone in the series is, in a certain way, a part of himself(https://evangelion.fandom.com/wiki/Mari ... note-:3-31). That way, Mari couldn't be introduced to fulfill a role his wife has in his life, at least not as the sole reason. Even worse, Hideaki Anno, his wife and the studio as a whole utterly despise the comparison(https://evangelion.fandom.com/wiki/Mari ... te_note-51) and the general notion that Anno's wife has some sort of control or influence in the creative process of the franchise. That way, considering Mari and Shinji to be in a relationship based on Mari allegedly being based on Anno's wife(https://evangelion.fandom.com/wiki/Mari ... te_note-52) ends up being a huge stretch.
Claiming that Sadamoto's manga is or became canon is just false
Some people have claimed that Sadamoto's manga was used as inspiration by Hideaki Anno and that it could explain a concealed interest on Shinji - regardless of the blatant lack of evidence in the movies. The thing is, even though it's already known that the manga isn't canon, being retroactively considered canon could only happen if explicitly said so by a source higher up in the chain of production - with Sadamoto being pretty much the #2 himself, that would be Hideaki Anno. The thing is, not only he didn't take part in the creative process of Sadamoto's manga - and if he actually had ended up liking Sadamoto's concept of Mari, he probably would - but Sadamoto was explicitly denied using Mari in his manga(https://evangelion.fandom.com/wiki/Mari ... te_note-44) in order to not interfere with her canon depiction - so much that he wasn't even aware how she'd end up being in the canon version - binding him to an extra, fanservice chapter in a manga that's already not canon. Anno's lack of approval or refusal towards Sadamoto's version of Mari(https://evangelion.fandom.com/wiki/Mari ... te_note-19) only reinforces the notion that he didn't care much because however Sadamoto depicted her, she would have her own canonical personality and background, and thus, claiming that her depiction in the manga became retroactively canon is simply false unless said so by Anno himself.
Now, to the best part: Mari and Shinji not being lovers is canon
Yes, I could have spared all of you of this wall of text and just have exposed the following, but considering a whole bunch of people won't even bother reading any of this to claim I'm wrong, I thought I might as well just expose many more arguments just because there are that many. Either way, it has been confirmed by, at least, three different sources that Mari and Shinji leave the station as friends. First and foremost, Maaya Sakamoto - Mari's VA herself - stated that she sees Mari and Shinji as being nothing but friends(https://evangelion.fandom.com/wiki/Mari ... te_note-15). She jokingly stated that she expects people to forgive her for holding Shinji's hand at the end of the last movie - and not for being paired with him - and also claims that Mari just really likes people. In fact, she states that the feeling she had as she acted is that Mari likes Asuka as a friend even more than anyone else
As exposed above, it's clear that Mari and Shinji are not actually a couple and their dialogue during the last scene is meant to highlight Shinji's change in behavior and serve a somewhat comedic purpose, since Mari's massive badonkers are kind of a running gag. Even though a relationship between them could be argued, that could only be so after the end of the movie, since the ending was meant to be open exactly so people can come up with their own versions of what's gonna happen next. If you want to believe they'll eventually end up together, you can. If you want to believe Shinji and Asuka will act on their mutual late confession and officialize their relationship, you can. If you want to believe Shinji will end up with fucking Ritsuko of all people, you can as well
The only reason I chose to write this is because I've been seeing a lot of people unfairly bashing either Hideaki Anno for the erroneous notion that he decided to pair Mari with Shinji or other shippers that didn't like the alleged couple. In the future I should write a post to expose my own interpretation of the ending of the last movie, based on some logical conclusions we're capable of making considering both in universe evidence and the general meta of the franchise, even though no one really cares - I just happen to have some spare time lately.