I have just finished a third EVA watchthrough, after several years, and it has struck me (as it happened the first two times) so deeply that my never left behind depression has come to knock back again.
While I can relate to Shinji under many aspects (especially regarding the relationship with my father and the lack of self worth), what really hit my soul is the deep sadness that surrounds Rei story arc. Even when she finally starts to create bonds with other people, to get a better understanding of others and of herself, she dies. And she s willing to, as entrapped in a no way out situation... til she regain full coscience of who her soul really belongs to.
But at this point I find tragic that the young girl that learnt how to slowly identify and express her feelings is literally no more.

Rei: But, there's someone else who is the true you.
Rei: You don't know her.
Rei: Because you don't want to see that, you are trying to run away.
Because of fear.
Rei: Because she might not have a human shape.
Because the present me might disappear.

Her true self is Lilith, and the young girl (what we, or at least some of us, loved of her) appears to be an inessentiality.
True, the memories of what happened are still with them (now in full), but what s left of the "almost human" Rei? Our Rei?
I like to think, for my own peace of mind, that the time spent as "almost human" wasnt a mere facade, that all her struggling wasnt in vain, as she GREW throughout the arc, as it was precisely that path that led her (and Adam/Kaworu) to grant Shinji (and to an extent, the whole humanity) a chance to decide for themselves. That OUR Rei is still there, soothening the Godly overhuman status of Lilith.

She has her moment on stage during Instrumentality, so I'd assume there's still a Rei as much as there's still an anybody in there. If she chooses to return to solid form afterwards is left to the imagination. Kaworu seemed to be at peace with being both a powerful angel/Adam-soul-carrier and being his independent self so I don't think it's impossible. A world destroying demiurge moon godess gifted with limitless power might not be content returning to life as a quiet teenager though.

She's simply not discussed at the end of the anime so everything you want really.

In the manga Rei situation is more explained
She says, you choose to return to your world (not our world). to Shinji
they hold hands she says she is happy to have met Shinji. What was empty he has filled. Rei has a cry
but i have to go
Is this the correct face I should be making in a situation like this (somewhat hamfisted becuse it looks expresionless when she was crying in the previous frame.
I will grant your wish
Rei explodes again
Rei's toughts I will dislocate myself and scatter myself and spread myself amongst all the creatures.
And now I'm waiting for your return
(Shinji has a short talk with his mom and dad and return to the world)

to those who have the manga is Rei having sex with a (near) unconscious Shinji (stage 93)?