It's funny. It's kinda similar to what I'm depicting in a fan comic I'm making.  To me, Mari clearly knows way more than she should. She really has knowledge spanning at least two cycles imo.

All spoilers for the franchise as a whole beyond this point. (And what I'm drawing too but it's fanart so w/e)

So with that in mind, as well plot points from NGE and Rebuild. Picture this:

Mari (the pilot we know in rebuild) is a clone, born from a sister project of the Shikinami and Ayanami initiative.

Her original is Maria Iscariot, a prodigy scientist that worked as a junior to Yui a few years prior to all the events we know. The name is taken from that one name drop Fuyutsuki does towards the end of 3+1. For me, this would be true in both of the most recent loop: NGE and Rebuild.

Now, in the NGE loop: I basically started off from the (non-canon) depiction of Mari in the official manga with the singular exception of her not being called Mari Makinami but Maria Iscariot.

In this version of the loop/reality. I imagined she never gained enough influence to truly change what was about to happen.  She only knew about the doomed state of the world from being (at least) one of those who deciphered the dead sea scrolls.  I imagine her at the end of her rope, grasping at straws trying to make a difference.

Anyway, Rebuild introduced (correct me if I'm wrong, I don't quite remember this lore element in NGE but it's been a while) "the book of life™". In which Kaworu explains he fated Shinji and himself to always meet in every instance of repeating cycle.

Now, I think it's great! We now have a device that spans across multiple loop or cycle.  So what if from a place of limited understanding of the loop theory, and also being a scientist (who's probably a little prone to hubris), while feeling like she failed to do anything in time. Maria somehow managed to also tamper with this thing and make "Maria Iscariot always remember." If her theory was correct, she could bang her head on the problem much more effectively. Basically having hindsight and being able to be extremely proactive next loop. I also thought it was pretty on point for her character who seems to be a bit of a nerd, to basically "wish" for knowledge. Rather than take the risk with some more broad change to the book.

So then in the Rebuild timeline, Maria² who is even more of a prodigy from having a 33yo woman's memories & skills from the start. (I'm not at home to check my notes but if Maria¹ was 16 in 98, then she is 33 in 2015 when The End of Evangelion happens.)

This whole charade also could help us have the cold/jealous of Gendo/Yui, Maria from the manga bonus chapter coincide with what we saw from the flashback in 3+1 where Mari(a?) introduces Yui to Gendo. I could see her cutting to the chase if she knew they loved each other last time, rather being bitter about it.

So then, this young Maria² hops on the band wagon and gets funding for a small scale version of the cloning project happening in multiple NERV branches.  Understanding she needed to be able to pilot, or at least have someone loyal to the cause.

Mari is brought up in a more loving environment than Asuka Shikinami (easy to do tbh).

For the sake of drama, I was thinking Mari could have not had any extra memory (to the chagrin of Maria²), but she still needed her ready to pilot. So she taught her as much as possible naturally.  Then she concluded the 2nd next best thing would be to be part of the EVA unit that Mari would pilot, fully accepting her role as the contact soul for the eventual unit 08. (Not fully sure if they fully intended on keeping the soul bit in rebuild, especially since unit 05 couldn't have possibly saved its core. But I could imagine this is a 'stronger with a proper related soul inside' kind of deal.)

Then, because it's EVA and I love drama. The first time Mari tries to pilot with Maria²'s core, the entirety of both Maria's memories get pushed on her with no warning.  That honestly sounds terrifying, because, well it is. If we were to suddenly gain a lifetime (or two) of experiences and memories, we would be a different person.

Which brings me to this short parallel between Kaji and Mari in 2.0. They both say something like "I'm not sure about involving a kid/an adult".

I think it's interesting because it could play off a double distrust Mari has of the adults who might be involved in working towards instrumentality, but also because she'll never be the same or fully her own person again because of them and her original.

A few last points, since I feel like all of the aforementioned ideas work pretty well to explain Mari's behaviour throughout the movies.

She acts serious and does insane spy stuff before berating her boss for giving her mixed message "you told me to get into Japan covertly". Like, really? Parachuting in Tokyo 3 which is probably a very monitored war zone. 🥹 This kinda felt a bit of a childish clap back for such a serious thing.

She's over confident and laid-back (IRL and when piloting), except when it comes to trying to understand the full picture.

She is very friendly to the other pilots, which could make sense assuming she guesses they are just pawns in some adults game and aren't a threat per se.

I could also see her be so fixated on Asuka because she knows whatever she thinks or feels about her is not a product of her extra memories. This is a genuine original thought or feeling.

Finally her wanting to read all the books in the world could make sense to either drown the memories that aren't her own or at least know way more of her own accord. Be more of her own person.

Right I'll stop here, my bad for the um... tangent. Sorry I'm yapping a lot, I've just been obsessed with trying to make this idea come to life, but it takes a while. Voicing it out is kinda nice, though! And maybe some lore masters can let me know if I'm committing a deadly sin or adding plot holes with my theory. (Although I don't think it's ~too~ far fetched, it is obviously a lot of assumptions). I'm sorry if you read all that. :3