We have here a very controversial series indeed. I don't know if the majority of CJAS would accept or reject this ending the way it is. I think I may be ambivalent - after all, we have been preaching for years that anime is not just about robots blowing each other up, it is an art form. Well, here you go, Evangelion is art containing deep psychoanalysis in which the "side story," the one about the Angels and Evas, was merely a vehicle, a background to carry it out. The background just happened to be so involved that nobody picked up on what Anno was really trying to say. According to episodes 25 and 26, Evangelion was a story about how Shinji came to accept the fact that he was worth something, no matter what others might think (or what he thinks others, especially his father, think of him). That's a lot in terms of character development for a 14-year-old boy.
This is not to say that Anno can get away with this scot-free. It is true that the director has total free rein over his product, but does that mean that he can totally ignore his audience? We wouldn't have so much of a problem if Gainax had not spent the last bunch of episodes prior to 25 and 26 depicting all the mysteries. If this series was about Shinji's personal growth, why was he so completely ignored since episode 21? Why did they put so much into those mysteries if they were going to abandon them? All this time they had said not to run away, and it turned out that they had "run away" themselves. The fact that Anno shaved his head shows that he indeed realized that it wasn't "right." All his other statements and his attitude merely sounded like he was self-justifying the situation. One reader of Animage did point out that, with all the pickiness about titles and subtitles, they neglected to put in the words "The End" at the end of this episode. Perhaps this meant that the writers did know that this was not an acceptable ending and that they were planning to continue in an OVA or movie (which they did). But that would be like submitting a really rough thesis to the readers with the thought, "Well, this doesn't have to be the final form anyway; I could fix it later and I don't feel like putting more effort into it now, so why don't I submit it the way it is?" Does this sound like professional behavior? Maybe Anno wanted to write his psychological story, no matter what others thought of him, but could they assume that he had no obligation to the audience simply because the medium is a TV series provided at no cost to the viewers? Do you think this is acceptable? Anyway, after all is said and done, whether or not you can live with an ending that is an artistic expression as opposed to plain entertainment will depend on your taste.
One final note, though: this episode did give the characters some sort of salvation that probably would not have been possible with a conventional ending. After watching all the terrible pain and suffering they went through in the second half of the series, it was a relief to get a glimpse of the happy life they could have had.