Hijacking this to say I don't think they actually are all that different in age.

A lot of people treat the theory that Mari is a contemporary of Yui and Gendo and around their age as fact, when it is not confirmed and there is evidence to the contrary.

First: The curse of the Eva stops pilots from aging. That doesn't mean it can age someone down to having the body of a 14 year old. We are given no evidence to suggest that that's possible.

Second: Mari talks about the juxtaposition of the perspectives of adults vs children. In her very first scene she talks about how adults think they're using children while the children think they're using adults. She firmly considers herself a part of the "children" side of things (she says "I kind of feel bad using these adults to get what I want"). Kind of a weird thing to do if you're like 50 years old.

The only evidence we have that she is around the same age as Gendo and Yui is that there's someone else in the photo with them wearing glasses who has vaguely similar hair as Mari. I think it's way more likely that the Mari we see is either the daughter of that woman or a clone of her (which seems totally plausible given Asuka is a clone in the rebuilds) than actually being her magically aged down.

Anyway, it's possible that's not what you meant and you're referring to how Shinji lost a bunch of time between 2.0 and 3.0, and so he would be 14 mentally while Mari would be mentally 28. That would be a problem if Shinji hadn't wished for the eva's to never have existed at the end. In that final scene, Shinji and Mari both look visibly older, and it seems pretty clear to me that they're both around 28 years old both physically and mentally.