This idea popped into my head last night.
Throughout the NGE series, Shinji basically has 3 solid relationships with women. Those women are Misato, Rei, and Asuka.
When Shinji was in an Instrumental state(EoE), these three women are also the three people that helped him affirm his identity and eventually "wake up" from the state.
This image of Misato, Rei, and Asuka overlayed over one another popped up once or twice in the Instrumentality campaign. It popped up because Instrumentality is the combination of all souls. This was reaffirmed when Asuka harassed Shinji about him jerking off over her comatose body, of Shinji watching Misato take it from Kaji, etc.
However, there is also a possibility that they all left Instrumentality, not only as the individual souls that they are, but as one soul. This could be perhaps due to Shinji's wishes or just due to the premature ending of Instrumentality. That soul could be Mari's.
At the end of EoE, you'll notice that there are symbols of Misato, Rei, and Asuka.
- Misato's cross is shown to be pinned up
- Rei is shown to be floating above the red sea
- Asuka is choked tfo
I know this image has popped up in the past but let's examine it from this point of view. We have Yui(Rei) and Asuka's mum, who happens to be wearing glasses that bear a striking similarity to Mari's glasses. So we have the 2/3 characters I've described from above in here, assuming that the glasses are an important representation.
Mari expresses a number of affectionate moments with Misato, Rei, and Asuka as well.
- Despite Mari being affiliated with SEELE, in Q she's on Misato's team. It appears Misato is opposed to NERV and SEELE in this movie. Further, Mari seems to have an idea of SEELE's goals throughout NTE... yet she still sticks with Misato.
- Mari and Asuka bond well on a number of occasions. Mari also has no issue with the intricacies of Asuka's Eva, and even mentions that it smells nice.
- Rei throws Mari backwards to avoid the N3 explosion Rei sets off in 2.
There is also the possibility that, of course, Asuka's mum's soul was pushed into Mari instead of Asuka's unit's core this time around. Asuka doesn't seem to show any powerful sync ratio throughout the series, nor has she mentioned her mommy issues yet. However, Mari pilot's Asuka's eva nicely, compliments it, and even removes the limiters on it, something we haven't seen throughout the series. Mari is seen wearing Asuka's mum's glasses and they only crack when Mari goes beast mode in Asuka's unit. While Asuka has the brawn of the series, perhaps Mari inherited the majority of the smiles of Asuka's mom. Or perhaps it could be an extension of the SDAT player theory, wherein Asuka's mom is contained in Mari's glasses(which they both shared).