It's more how they approached things.
It's as if a story like High School of the Dead ended with "...and then he woke up and it was all a dream".
Messing up everything and then restoring everything by 'traversing through an alternative universe' is really double you tee eff for the type of story.
They may as well have had a necromancer revive Nagisa as a magical girl.

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Really guys? Although I considered the very end (of the last episode) surreal and slightly unusual - I never had an issue with the conclusion of the story you guys seem to be having.

Consider what happens to Tomoya when Nagisa passes away and how he changes - this is the whole point of this part of After Story - he learns a lesson in the appreciation of life.

He lost the most important person in his life and after that, he felt he had nothing left. This is what drove him down into the misery that consumed his life afterwards. When he finds a place for Ushio in his heart he realizes his mistake. Of course, it's not easy - losing someone that important to him must have destroyed him and it seems like his love for her was such that all that was left inside him was sadness.

The important thing, was that he realized that with Ushio he could still be happy and, of course, it must have really clicked that Nagisa was in Ushio in many ways and as they started to interact without the regret he must have felt towards her up until that point, he realizes not only his mistake but the fact she can be the light in his life. When he realizes the error of his ways, he changes fundamentally and what followed, what happens to Ushio, followed. Perhaps it was in part due to the neglect he showed towards her for so very long... I couldn't imagine, after creating the bond he did with his daughter, how it could have possibly felt to have every last degree of happiness taken from you.

The resulting miracle brought this family back together, yes, but it seems as though the whole process was something he needed to experience in order to live the life he desired. I mentioned the regret he felt towards his daughter: there must have been feelings he had when Nagisa was slipping away while giving birth to her that he shouldn't have had, so he had to learn to accept what must have been Nagisa's last wish, for him to be with Ushio no matter what. To be a family regardless and find happiness even after she passes away. He failed, but he ultimately learnt from his mistakes, but he was punished yet again because of the fact that even if Nagisa wasn't there, Ushio should have been just as important to him from the start, but she wasn't. Realizing she should have been and realizing the relationship he had with his daughter and losing everything after finding it was the trigger for the return to the most important moment in his life.

She survived, and they could live as a happy family, but even if she passed away, he wouldn't have felt the regret he did for having a child with Nagisa and he would have loved his daughter through the sadness of losing the one he loved most and as such, he wouldn't have lost himself in it either.

It seems as though by learning this most important of lessons he found himself in a reality where he could truly appreciate the happiness he had and not take it for granted. (Of course, the happiness he sought was represented by the balls of light that appear.)

As a whole, the story is incredibly deep for an animated title and I could imagine, like myself, it affected many others significantly. There's a lot people can learn from in the story that is told, and the most important one is to appreciate the happiness you do have and to cherish it, and it's just as well that wee appreciate the story for what it's worth - an awful lot, at least to me.