I have found this to be a difficult question. Anno's statements on matters like this are in my experience vague and not always easy to reconcile. This is my best attempt at trying to work it out. Please keep in mind it may be very incorrect! I'm going to use the following notation:
25/26 - broadcast versions of episodes 25 and 26
25'/26' - EoE versions of episodes 25 and 26
25*/26* - originally intended versions of episodes 25 and 26
One of Anno's most detailed statements on the ending comes at the end of the first June interview. There is a translation here, but some important parts are hard to interpret in the original (for me at least) and consequently in the translation. Generally, though, Anno seems to be saying the TV ending was intended for one episode (26*) and there was one further plot-related episode (25*/25') which didn't get made. In describing the intended ending, however, Anno seems to be referring to the content of broadcast episode 25 (seeing the parts of other people that they want to keep hidden) rather than the content of broadcast episode 26.
庵野 [中略] ２５話で大体の謎にカタがついたら、あとはシンジさえなんとかすればいいやと。
Anno: ... I had thought that, once I had resolved most of the mysteries in episode 25, I could do something with Shinji just by himself afterwards.
From moyaofthemist's translation:
Anno: ... The idea of a play within a play and making it like a stage came to me at the last moment, but Shinji-kun went on looking at not only the surfaces of strangers, but their pasts… No matter what kind of person it is, is it not the case that they have filthy aspects? But I think that when you have a relationship with someone, particularly at the moment when you think that you don’t want to be hated, poof, you take on the burden of doing everything you can to keep from showing that part of yourself. You try to show as many of your good aspects as possible. It’s not that you judge while looking only at those sorts of aspects, it’s whether you can ever look at that human as a single individual at the times when you see that person’s negative aspects.
Interviewer: It’s like, can you accept them in their entirety?
Anno: Precisely. That’s Dr. Freud’s theory of a good mother and a bad mother at the oral stage of development, though. In short, a mother is someone who simultaneously protects you unconditionally and restrains you—which you could call the bad part. Additionally, it’s not the case that a mother is in a good mood every day. For example, when you cried, if she was in a good mood, she might have said something like, “Be a good child, a good child; you mustn’t cry,” but if she were irritable and in a bad mood, she might even shout, isn’t that right? From a child’s perspective, you can’t see the two as the same person. Therefore both a good mother and a bad mother exist, and when you recognize that they are contained within a single personality, you’re able to see for the first time what’s known as a stranger [other]. I intended to do that. I was able to release all of the ideas I had.
In an interview with Waseda University in 2000, Anno says the following:
Anno: It was a question of, this was probably how it was supposed to be originally. That was [the basis for] the remake. What I really wanted to do was episode 25. Originally, I had planned that the television version of episode 26 would end up being like [it was]. It would have been beautiful to do the story properly up to episode 25 and then turn everything inside out with episode 26. 25 fell through, and in the end I felt we had to [finish] producing the series as things were. For the film, the main thing was that I wanted to remake episode 25. Episode 26, I thought I would beautifully recreate. I didn't expect at the time that Ayanami would become enormous, though. I felt, well, if we're going to do it let's make her the size of the planet. [unclear on last sentence]
- I thought the television version of episode 25 was interesting. How does it seem when you look at it now?
Anno: I didn't really watch it when I made it [? lit. put it onto film]. Episode 25 was the original final episode.
This does seems to contradict slightly what Anno says in Parano, so I wonder if I am understanding it correctly.
庵野 [略] 二五話って、最初にフィルムができて見た時、自分で、俺天才かなあと思ったんですけどね。でも、後からもう一回編集して見直すと、ウワァ～！全然ダメだとガッカリして。
Anno: When I saw episode 25 after first putting it together [lit. when the film was first completed], I thought, “I’m a genius.” However, when I re-edited and re-watched it afterwards, I was crushed. It was no good at all.
In addition, in his late commentary, Oguro says that his staff had the concept of the series' ending explained to them (he thinks) in January 1996, so the idea for the ending was in place at least by that point (which was still rather late!).
I think it was January 1996 when the LD commentary staff got together for drinks. There were some people from Gainax with us, and they explained to us the content of the final two episodes. That was the first time we learned of the contents of the final two episodes. According to the explanation at that time, the main characters would each take turns appearing on the screen, and we would be told why [or maybe in what way?] that character had to be complimented. The individual characters were samples proving that human beings were an imperfect existence. Since we had already had a few drinks, we thought this was some kind of joke and didn't take it seriously.
Bonus anecdote ^^:SPOILER: Show「第弐拾伍話 終わる世界」を観た時の事はよく憶えている。当時、僕や幾原邦彦監督は『少女革命ウテナ』の準備を進めており、『ウテナ』のスタッフルームであるビーパパススタジオをすでに開いていた。第弐拾伍話のオンエアは、ビーパパススタジオで皆と一緒に観た。第弐拾伍話を観て、僕達は盛り上がった。その前衛的な手法とフィルムのテンションの高さ、そして、次に何が起きるか分からない事を面白いと感じ、感銘を受けたのだ。「次に何が起きるか分からない」なんてよく使う言い回しだが、アニメを観ていて本当にそんな事を思ったのは、この第弐拾伍話が最初で最後かもしれない。勿論、この話を観たファンが困惑するであろう事も分かっていた。
I well remember first seeing episode 25 ("A World Ending"). At that time, I was working with Director Kunihiko Ikuhara on the preparations for Revolutionary Girl Utena; we had already opened the Be-Papas Studio, which served as the staff room for Utena. When episode 25 was broadcast, everyone was watching it together in the Be-Papas Studio. Watching it, everyone was enthused. The combination of avant-garde technique with the high level of filmic tension, together with the feeling that we had no idea what would happen next, made a deep impression upon us. "Not knowing what will happen next" is an expression people use all the time, but that was probably the first and last time I honestly felt that way watching an anime. Of course, I also knew that the fans watching the episode would be bewildered.
There seem to be some substantial differences between Oguro's account and Anno's description of the finale in the JUNE interview. That being said, it also seems that both Oguro's (imperfectly remembered or conveyed?) account and Anno's description give primarily details of what happens in broadcast episode 25. This seems to suggest that the contents of broadcast 25 were drawn from 26*.
What seems certain is that the originally intended 25* was remade as 25'. What seems possible is that the originally intended 26* corresponds substantially to 25. What is unclear is a) what part of 26 belongs to 26*, or what the general relation between 26 and 26* is, and b) what the exact relation is between 26' and 26* on the one hand and 26' and 26 on the other.
My guess for the moment at least is that 25*/26* corresponds roughly to 25'/25, but I am not sure. Oguro has a very strange theory that 25 and 26 are not really connected and are in effect different endings, and that the end of 25 can serve by itself as a conclusion to the series. I think it's not impossible that 25 by itself corresponds to 26* and that 26 is an additional invention, but it's also possible that 26 was in fact included from the start in 26*, as at least some of Anno's comments seem to suggest.