Dr. Nick: Now that the series has finally gone full art-house, we should briefly tackle the big production side question: why is the ending so art-house? Just by watching the show, it should be clear that we're dealing with a singularly director-driven, deeply personal work. It is also a famously well-known fact that the said director has claimed there was nothing wrong with the TV ending, as immortalized by his "Too bad" statement that probably cemented his auteur bonafides.
Then again, it's no secret that the show had major production issues towards the end. The creators talk about this meltdown rather coyly, but they have no qualms admitting that they weren't able to follow the originally intended script. As detailed in the EoE movie pamphlet (AKA the Red Cross Book):
The movie ep.25 "Air" is based on the script already in place during TV production originally intended for TV Ep.25. Because of various problems during production, this script was not used and the TV Ep.25 "The Ending World" was done in a same way as TV Ep.26 in which the drama was developed within an internal mind universe. Because of this, it could be said that this ep.25 is a return to the original intended story. In contrast, the movie ep.26, when compared with TV Ep.26, contains much more content on the story and plot, thus deepening the theme brought out in TV.
It should therefore be uncontroversial to say that the last two television episodes are quickly cobbled-together replacement things that share a family resemblance with the more mundane clip show episodes of the era. But as with all artistic things, it's the reception that matters, and these two episodes were infamy boosters of the highest caliber. Consider a parallel world where the production issues weren't so overwhelming and the intended story scenario stayed on track, resulting in an EoE-lite TV ending, with perhaps two or three compilation movies afterwards. Somehow I doubt Evangelion would have gained the same levels of cult following in that situation.
UrsusArctos: There's a rather heavy dose of reality subtext that Gainax wanted to avoid. Episode 25 aired on March 20, 1996, exactly a year after the infamous Aum Shinrikyo doomsday cult killed 13 people and crippled many more on the Tokyo subway using sarin nerve gas. One major unspoken reason for not sticking to the original Episode 25 script was because the sight of the headquarters of a pseudoreligious organization being stormed by Japanese authorities - which happened to Aum soon after the gas attack - would have seemed like something ripped from the headlines and insensitively placed center stage in an anime series that already sailed disturbingly close to the wind when it came to referencing the state of Japan. Evangelion would have gained infamy, all right, but not of a sort anyone would've wanted.
