The other great inconsistency is in the matter of Adam. In episode 15 the being later identified as Lilith is named Adam, and indeed it seems for much of the show that Gendou & Fuyutsuki mean precisely this entity when they talk about Adam- even though they should know more than anyone else that it's Lilith.
For a long time I thus supposed that until some point well into Eva's production, the story concerned only a single Seed of Life, Adam, single alien vessel, the White Moon, and that Humanity (we cannot call them Lilin) were collectively the Second Angel. The more complicated backstory involving Lilith was likely devised after episode 15 finished production. However, this account leaves an enormous gap- namely, who Rei was supposed to be, if not the avatar of Lilith. Merely a clone is an unsatisfactory answer; straight from the start Rei is a divine being of some kind. The only solution I could think of was that she was supposed to be the avatar of Adam, which seems quite unnatural.
I now propose a somewhat more complex conjecture, based on the following considerations:
*The entity in Terminal Dogma being called Adam until very late.
*Shogouki being compared to Adam, until the sudden explanation that she- the essential Eva who should be made from Adam- is in fact made from Lilith.
*Ritsuko's story in episode 23, which has humanity finding "Kami" at the South Pole, and then making/finding Adam out of, apparently, what was left of "Kami" after Second Impact.
*Humanity (Lilin) not being descended from Adam, which is somewhat odd.
*The GeoFront lacking any indication of being an alien structure until quite late.
*There being only one ancient Impact, despite Adam's & Lilith's arrivals presumably being separate events.
*How in the Second Episode 24 draft, the familiar Terminal Dogma scene plays out without Kaworu ever realizing that "Adam" is Lilith. Nevertheless, immediately after this we have a scene where Kiel references Lilith's role in Instrumentality. This suggests that Satsukawa while writing the draft knew something about Lilith, but thought that she was something other than the Terminal Dogma entity!
*Rei, and thus Lilith, being present from the beginning.
I thus suspect that until quite late in Eva's production (apparently as late as the final draft of episode 23), the backstory was something like this:
There was a single Seed of Life in Antarctica, Kami or Adam Qadmon, consisting of masculine & feminine elements bearing the Fruit of Life & the Fruit of Knowledge. The Angels were made with the Fruit of Life, and Mankind with the Fruit of Knowledge. At Second Impact Mankind attempted to acquire the Fruit of Life from Kami. Instead, Kami was catastrophically split into their two component beings, Adam and Lilith. Adam lost the Fruit of Life and was reduced to an embryo (imperfectly cloned into the Eva Series). Lilith seemingly retained the Fruit of Knowledge, and she was brought to Japan. There she was bound, armored, and had her soul exchanged (accidentally?) with Yui's- thus Yui became Lilith, and Lilith survived in a regenerated version of Yui- Rei Ayanami. Yui-as-Lilith was then redesignated as Eva-01, being the other half of Adam.
Conjecturing as to the original ending, clearly it would have involved Gendou's plan to recreate Kami by merging Adam & Lilith. I suspect that Gendou planned to merge himself into Adam (that is, the Adam embryo now regrown in Terminal Dogma) and join with Yui-as-Lilith as the new Kami. What role Rei would have had in this version is unclear to me- it's unlikely that Gendou would have cast her aside. The best solution I can think of is that Rei and Shinji, the two Ikari children, would have been made into a new Adam-Lilith / Kami pair to procreate on a new world. Alternately, Gendou-Yui-as-Kami would have traveled to a new world, leaving Shinji & Rei together on Earth. Needless to say, this is highly speculative.
My guess is that the plan was altered rather late, as the last three episodes were being written, seeing as 23 clearly uses the older paradigm. I'm not sure what motivated this- Kaworu isn't clearly Adam until the DC/EoE.
*Two primordial vessels- the White & Black Moons, with two primordial beings, Adam & Lilith, in conflict.
*Lilith's arrival in the Black Moon created the Moon (the celestial body).
*The Angels are descended from Adam, the Lilin from Lilith.
*The Evas are made from Adam, with the exception of Shogouki, who is made from Lilith.
*Lilith is in a clone of Yui (Rei), while Yui is in a clone of Lilith (Shogouki).
*Kaworu is the avatar of Adam, and Rei is the avatar of Lilith.
*Gendou unifies with the Adam embryo but apparently plans to hand everything over to Rei.
*Later Adam & Lilith- with their original souls- are unified as a Kami, and Shogouki, the daughter of Lilith, likewise joins with Zeruel, the son of Adam, as another Kami.
*Both Lilith and Shogouki are used in Instrumentality, though either would be sufficient.
In the earlier version, we would have had:
*One primordial vessel in Antarctica, with a single hermaphroditic Kami within.
*Kami's arrival created the Moon (the celestial body).
*This Kami then procreated Mankind and our siblings, the Angels.
*At Second Impact, Kami was divided into two beings, Adam & Lilith. Adam was reduced to an embryo and used as the basis for the Eva Series (later he was regrown in Terminal Dogma)- he had lost of the Fruit of Life. Lilith, meanwhile, was armored as Eva-01.
*Lilith & Yui thus swapped bodies- Lilith's soul was placed into a regenerated Yui, while Yui now inhabited Lilith's body.
*Kaworu(?) is the avatar of Adam, and Rei is the avatar of Lilith (it's unclear even in OA 24 that Kaworu is Adam himself). Alternatively, Rei is the single avatar of Kami as a whole.
*Gendou unifies with Adam to join with Yui, who is Lilith.
*Third Impact would involve (in Gendou's scenario, at least) the reunification of him-as-Adam and Yui-as-Lilith as Kami.
*Both Lilith and Shogouki are used in Instrumentality, since they are the same being.
One will also note the similarities this has with the lore that seems to be at play in NTE.