sci-fi references that are made include...
It's worth noting that the Japanese fan community view of Western SF differs from that of native speakers. One quite relevant case is E. E. 'Doc' Smith's Lensman
series, which in various forms (often less than properly licensed) remains to this day way more popular in Japanese SF circles than in its native America (to the extent of having updated editions in which the original 1940's tech -- such as the computers being the girls cranking the adding machines -- has been overhauled for the contemporary reader).
While 2001 has evolutionary uplift by remote god-like extraterrestrials, the Lensman
series adds explicitly a single primordial super-civilization seeding the galaxy, and has group-minds and minds-wide-open telepathic conferencing amongst the next-step and near-to-next-step sophonts.
I don't disagree at all. However, I think it's a pretty big leap from "this probably influenced their work" to the fairly detailed proposal you and NemZ have advocated in the past.
Two levels here -- what the author intended; and what the viewer sees.
In the former case, we know the story was to some extent being made up as they went along, part of the structure we see is going to be post hoc
rationalization, as much by the creators as by any of us.
With just the TV series (and the extra-textual knowledge that this is made by a studio full of SF fans) -- all its obscure hints about Gendo's master-plan of apotheosis, and its other casual dropping of genre cues
A cavern left behind by someone, who was not us.
that suffice to tell us that the GeoFront is a Forerunner artefact -- a reading of the ending on equally SFnal terms as upload (or, dropping the pure materialist notion in favour of NGE's dualist model, soul transfer) to some unspecified substrate (perhaps EVA-01, if we take a hint from various asides in EoE) is natural.
With secondary sources like the NGE2 game (and its various end scenarios) I feel it's reasonable to assume that something along these lines was intended, even if only along the lines of "Let's use Gendo's hinted master-plan to justify putting the characters into a wide-open N-way so we can do the last two episodes as abstractly as we need, given the budget."
As I said to Symbv, though, replacement ending != alternate continuity. It's more "this is a replacement ending. The same events occur, but the movie approach uses a slicker format to make the fans happy."
By replacement, I meant unplug the old and busted one and discard it -- and that seems to be the approach taken by the Japanese fan-base.
When I first saw EoE, the cognitive dissonance of trying to hold the two endings into the same continuity became, as I said, too much to maintain towards the end -- in the one, Shinji is happy, and with others; in the other, distraught and isolated. Knowing now more about the circumstances of the productions, it seems likely that the harsher treatment of the characters, and the different and downbeat end are the fingerprints of Anno's later bout of depression; and that in each case Shinji ends up roughly where Anno was at the time.