Kishimoto.... What the hell went wrong?
He had years to change the course of the story, develop new storylines and shift fans' support to one end pairing. And it's a backhanded verification to say that because NH was such a 'shocking ending' or 'climactic finale' or however they put it, NS must have been the OTP. It wouldn't be a shock or final twist if everyone expected NH to happen.
My theory is that several things happened in the end:
- Kishimoto signed over the story rights at some point, and probably before RtN - Just before RtN, the powers over him had not seen any commercial value in directing the course of the manga. But something changed with RtN. I think the success of RtN made them sit up and think a bigger, splashier ending would bring in more money and drive new fans back to the manga.
- I think Kishimoto is much more jaded at 40 than he was at 22-24 when the manga started - In the end, Naruto did not reach his goals of the beginning. He did not get his first love, and he did not become the Hokage in his own fashion. Instead he is part of the cycle, and he is shown eating at his desk, drinking on the job and spending too much time away from his family. Basically a self-portrait of Kishimoto himself, as well as vast multitude of "salaryman" workers across Japan who work the same grueling hours and lifestyle.
- I think Kishimoto is rebelling against the way he's been forced to end the manga - By keeping the NS going strong then just slapping on an ending that was vastly different from the build up, I think Kishimoto was pushing back against the new direction of the series, in the only way he can. He continued to write/illustrate what he wanted and then gave them the ending they dictated so it would line up with the movie and new series. He's basically letting fans interpret what they want.
- I think Kishimoto is rebelling against the fans - I think the leading interview questions, the clamoring otakus, the publicity circuit for an ending he wasn't please about and a movie he didn't create have left him bitter. I think he is answering whatever he feels like at the moment, and maybe even giving misguided answers if the interview questions are tremendously one-sided. Like if an interviewer asks something that might be flattering to Hinata, then Kishimoto answers with something unflattering. Because every interview has been flat and filled with semi-negative statements. These are not the glowing, effusive answers of someone who is pleased and proud of the outcome of his series.
- I think if Kishimoto had his way, then "The True End" would have been the end — Kishimoto loves his tragic stories. And I think he included that chapter in there, with that highly suspicious title, as a way of saying this is the way he would have done it. Sasuke and Naruto would have died in the end, just as Naruto predicted. The cycle of hatred would be broken by their deaths. The epilogue would have Sakura would mourning Naruto's death along with everyone else, while privately dedicating her life to continue his legacy, just as Konan had done. Hinata would have turned into a strong leader for her clan, using Naruto's nindo as her own. Karin would mourn Sasuke, who would now be seen as a redeemed hero for Konoha as well, then she be shown finding her own fulfillment. Then the next generation of would be shown carrying out their legacies. Every story in Naruto is a tragedy. Every story is marred by unfulfilled goals. This is what Kishimoto gravitates toward again and again. Not the romance, I think it's the happy endings he's bad at writing. So I think his 'true ending' would have been a loss of the hero, but the survival of his will.
I don't think there's a magic bullet explanation. Instead there are a lot of puzzling actions and contradictory messages from this ending.
Even the conclusion of the series is a lie! It's not actually ending, just carrying on in another form. So much so that at the end of the movie aptly titled "The Last" they say there's going to be another movie!! It's really crazy.
Ultimately I think there were too many cooks in the kitchen. There clearly is a huge difference between the tone of the manga, and the direction of this newly launched version of older Naruto and company. Kishimoto was closely involved in the series, and now he's just along for the ride with the new projects.
Maybe at some point Kishimoto will speak honestly about what really happened. Maybe not. But I think his careless answers in interviews already speak volumes about how he feels about the end of Naruto. Whether he cared or not, it doesn't matter. It's been out of his hands and moving in this direction (toward the movie, etc.) for a really long time. And now I think he just wants to be done with it all.
Any other theories as to what went wrong, and when?
Persona 5 hype 
The Gold Saints
