Still, I see the end of EoE more as an alternate ending than a replacement - I think both have their merits but display different attitudes towards the same idea.
I guess my own view of Evangelion's ending(s) goes along these lines:
It's difficult to argue against the idea that budget shortfall, to a greater or lesser extent, must have shaped the ending of the original series. (Although Hideaki Anno has denied even this.)
But what puzzles me is: End of Eva is basically four times the length of an episode. How could Anno have told the kind of story presented in the film in only 50 minutes of TV, even if the budget
had been available?
Given this, I think there was surely
some degree of abstraction intended from the start. For me, the original concept for that was perhaps somewhere between the freeform freefall that makes up the entirety of the final episode, and the much shorter equivalent segment found in the latter part of End of Eva. (This time using live-action footage as its way of shaking up the format, given that Anno had already played scratchy, low-fi drawings as his wildcard in episode 26. It also no doubt doubles up as another useful budget saver.)
Anno has already dealt animated deconstruction from his hand before with the conclusion to Gunbuster, I understand. Either that was the prototype of an idea he would fall back on a second time, or he messed up the budget calculations for that show too! I'd be able to dissect that part a lot better if I'd actually seen the series, but alas I don't own a copy of the UK's glorious tape-transfer DVD of Gunbuster.