Aeon Natum Engel/WMG

ANE is a result of Instrumentality.
What? Someone had to get the obvious one out of the way.
 * Earth Scorpion: Hmm. So, presumably, Aeon Natum Engel was produced when a successful Yui-led Instrumentality rebuilds reality, leaving the characters from the original Eva as the Outer Gods.
 * Yui = Azathoth: She's never actually present, but everything happens and occurs because of her, even as she sleeps in Unit 01.
 * Gendo = Nyarlathotep: He's a dick. Also, he does Yui's tasks, as befits the soul and messenger of the Outer Gods. Also, he's a dick. Big point here.
 * And this is where the theory breaks down, as I can't think who would be Yog-Sothoth. Maybe Rei, stuck on the outside, observing, as we saw in Instrumentality, present at every death, yet doing nothing to stop it.
 * Wait, what do you mean, "I'm the author". Damn it, I can WMG my own fics, right?

The Replica Elite are Rei-clones
We know that they're female, unlike the canon ones, and they're a product of the Herkunft Group. It makes sense that they're using her as a template, especially given the things that they pull on the Nazzadi Loyalists.

Alma is going to start chasing after Kaji
He's infamously good with the ladies. Wouldn't it be terrible if it backfired against him?

Alma is going to start chasing after Shinji
The poor kid generates an Unwanted Harem in canon. A creepy, dead, ghost-girl with no sense of personal space just makes things worse for him as a Butt Monkey. And raises the question of what the hell you call a relationship with the rage-fuelled ghost of the mother of a person who was created also using genetic material from your mother.

Alma is going to start chasing after Asuka
Because no-one would ever expect it.

Alma is going to start chasing after Rei
For same reasons as for her chasing after Beckett.

Aeon Natum Engel is set in the same universe as Spore.
Spore takes place more than a billion years after ANE. The reason why Earth is deserted is because Alma killed everyone, and The Grox are the Rapine Storm. When you go into the center of the galaxy and talk to "Steve", it's really Alma you're speaking to.