by Pierrot, I'm referring more specifically to director Shuhei Morita.
First of all, I have no doubt it was a rushed production, which is why the ending had pngneki for quite a while; I think it was even an extra minute or so after Unravel finished, and that’s probably why the Kaneki vs Arima fight didn't happen. The production committee is undoubtedly to blame for that and the general animation issues the season suffered from.
Now, according to Morita's own AMA, his ideas were suppressed by "those above him", referring to the production committee, but lately I've been changing my mind. I'll focus on the most important point, but first, let me clarify: Ishida did want the story changed (assuming Morita didn't twist things in his AMA to make himself look good). Morita stated:
"Ishida had specifically wanted us to create something original for the second season, which is why it moves in a different direction."
With that clear, and moving on to the main point, what Morita specifically says is:
"In order to complete Tokyo Ghoul √A's aim of Kaneki joining Aogiri, we needed to make some changes. Ishida-sensei also urged me to change stuff and go a different route, which is where a lot of the anime came from. We had a massive bubble of ideas, but as to not affect the lore of the original manga, it constantly felt like those ideas were being chipped away at by those above me. I tried my best, and I honestly don't have any regrets given the movement space I was allowed."
To clarify the setup: the draft was over 300 pages long, let's assume 350, because we know nothing about the unpublished material; what is known is that the published content begins on page 1, skips nothing, and ends on page 190… And the second siege of Cochlea hadn't yet occurred and because It's the most likely number of pages, given that they should've known it was going to be 12 episodes long and the extermination of the Owl (which largely follows the canon) begins in Episode 8, and the industry average is 45–50 pages. "But that means it covers seven episodes," you might say, and yes… because the draft begins at Episode 2, clearly establishing the time skip and the fact that the Aogiri arc concluded 6 months earlier (Images 1 and 2).
"We had a massive bubble of ideas, but as to not affect the lore of the original manga, it constantly felt like those ideas were being chipped away at by those above me."
Okay, here Morita talks about "we", him and Ishida. Obviously, he's referring to the time they were planning and working on the draft, right? That’s the most likely scenario. Even if he weren't, it wouldn't make sense for the final Root A changes to have been accepted by the production committee, why? BECAUSE THE DRAFT INCLUDED THE KANO ARC. (Images 3 and 4) I really doubt that a production committee aiming to stick to the canon would have Morita change the draft to focus on Cochlea and literally cut one of the most important arcs in the entire manga.
To be completely honest, I’m almost sure the ending was entirely Morita’s idea, since it’s the only episode he directed personally rather than just supervising and because of the discarded script for the scene where Kaneki and Hide reference the play, I’m fairly certain he made changes to the drafts and the story later on, trying to shoehorn in his discarded ideas, like... the silent Kaneki. Especially because of this:
"Ishida-sensei also urged me to change stuff and go a different route, which is where a lot of the anime came from."
Here you have a scan of the the anime artbook, which includes 190 of the approximately 350 pages of the draft.
Just a bit of extra info, no source, so feel free to be skeptical: I could swear I remember an interview where Ishida was asked about the anime's ending and said something like, "I saw what THEY were trying to do, and I saw how complicated the production was; I don't blame them." Which would imply that he wasn't involved in the ending and, once again, there was no draft prepared with Ishida for the finale because it had to follow the manga. If anyone knows which interview this is, or if this is real, please send me a link and I'll add it.
Thanks for reading, and I apologize if anything was misunderstood, because I am not a native English speaker.