This is why I feel that the TV ending as a stand-alone becomes much tighter thematically. EoE casts all those doubts you expressed, because even if the 'main theme' is about one thing, there's all these other factors and issues highlighted by the film. This isn't a problem in the TV version because
-It's pretty much all about Shinji
-The way it's presented (a stroke of genius) is such that the thematic and character psychology concerns become all of the concerns. We don't have to deal with what happens to Asuka in the beach, or whether or not people in general will actually try to become individuals again.
Of course it also ends much more conclusively with the 'Congratulations', instead of two half-dead broken people trying to strangle each other on the beach of the apocalypse. I think, as a single piece of work, EoE is cooler than the TV show because it's a well-directed film with land-mark and revolutionary action animation, but as an ending to the 24 episodes that came prior, it's not nearly as powerful and lacks that boldness of the original (whether or not it was due to production constraints is perfunctory, really, considering they could've just done the same thing everyone else would do, release the episodes half-finished).
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...I feel like I insisted enough with this so I'll let it go after this post, lol.