Part of me wants to explain why this arc is so amazing, but everyone else here echoes my thoughts. In my humble opinion, this is the most compelling, insightful, tear-jerking story Key has ever produced.
Therefore, I’ll try to list some of my gripes with this arc instead. Most of them are minor, but a couple weren’t noted previously, so I believe it’s worth visiting.
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Although After Story was slow-paced, I didn’t feel most of it was filler. I believe almost every scene existed to convey a specific thought or feeling from the characters involved. I cannot in good faith say this is true about the beginning portion. Nagisa’s attempt to keep the drama club going after Tomoya and Sunohara left was dragged out and unpleasant to read. In spite of how much she’s grown as a person, she’s only able to get a reluctant club adviser and fails to confidently deliver her orientation speech. It makes me feel like Tomoya’s efforts to make her more assertive and branch out were in vain. I know considering how drama is unpopular at Hikarizaka, it would be tough for her. But I feel the writing over-emphasized Nagisa’s struggles, almost as if she was kind of new to this. Is she really THAT reliant on Tomoya that she can’t autonomously function? I doubt that’s supposed to be the implication, but it’s there nonetheless.
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Akio’s perverseness. Haah… I love Akio. He gets a lot of funny and heartwarming moments in this arc. But the revelation of the porn magazines he’s hiding from his wife, the lewd pictures he takes of Nagisa, and peddling one of his porn magazines to Tomoya because he believes the latter is sexually frustrated was all in bad taste. I know Clannad’s a quirky comedy series a good chunk of the time, but Akio spends a lot of time poignantly participating in the grounded drama of the series. It’s hard for me to like him when the writing implies he’s perving on his daughter, even if the implication is he may be exaggerating some of it to see Tomoya’s reaction. And on a side note, I really wish choosing all the chaste options in the “Does Tomoya wanna be a perv?” story should allow Tomoya to reject Akio’s porn magazines without awkwardly lusting over Sanae’s panties, prompting a Little Busters-esque battle in which they see who is the manliest. I mean, we get a not h-scene that’s kinda uncomfortable; I feel I was cheated out of the opposite. The anime made the right decision in adapting these elements out of the character.
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Echoing a number of people here and elsewhere, I like how the anime handled the reason they don’t bring Nagisa to a hospital better. I understand the sentiment, but when both your life AND your baby’s life is at stake, you need to take every precaution possible. I feel Maeda didn’t need Akio and Tomoya to be bowled over in this aspect to prove Nagisa’s strength, either, because wholeheartedly rejecting the idea of an abortion conveys that idea well enough.
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Being the free-spirited, emotionally impulsive person he is, Akio would have gone out of his way to knock Tomoya out of his funk after a couple months. There’s no way he would’ve passively waited for Tomoya to do it himself (and even then, Tomoya was spurred on by outside sources anyhow). I can agree with him taking care of Ushio without complaint for a little bit of time, but once he realizes Tomoya isn’t growing out of his depression, he would confront him. Whether violently or not, it would be intense. I can forgive this a little bit, because scenes like the Field of Flowers could not have been surpassed by this confrontation, but it’s more in-character for Akio. He’s just not the kind of guy who would let Tomoya’s shirking of responsibility stand.
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I appreciated how Tomoya and Nagisa visit Naoyuki in a scene that surprisingly enough, didn’t make it to the anime. It effectively foreshadows the trouble he’s getting into. However, his mini-arc post-Nagsia’s death felt cheap and over-the-top. It’s like Maeda recognized how unlikeable the character was and decided to do everything in his power to make him seem like the most sympathetic character ever. It didn’t work for me, I’m afraid. Shino’s appearance wasn’t properly built-up to, her story basically hand waves Naoyuki’s failings as a parent because he “tried hard” (rejecting those close to you who want to aid you in your emotionally-wrecked state is quite the responsible decision. Even Tomoya knew better), and making Tomoya feel 100% in the wrong for disliking him. This is made worse by how unapologetic and victimized Naoyuki seems to think he has. I know the guy is broken, but couldn’t you at least have him acknowledge he made mistakes to Tomoya? The latter’s bawling at how poorly he treated his father, in spite of the many transgressions his father committed. It left a really bad taste in my mouth.
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The standard end was poorly constructed. Ushio’s sickness emerges out of nowhere because Maeda wanted to write her death scene. As cynical as it is of me to say, it had no emotional impact because it wasn’t built up to. There was no foreshadowing that she would inherit the disease, and worse, at this point, no one needs to grow. Not only was Nagisa’s death properly progressed to narratively, but it also served to expose how weak and frail Tomoya really was. Now that he’s realized from friends and family that life is worth living regardless, why does he need this additional pain? It just rings very false to me.
As with many of you, I agree that the ending is narratively and thematically sound. In addition, I admire the many people on this thread who are smart and thoughtful enough to analyze the extremely abstract nature of the light orbs, the Illusionary World, and how it relates to the events of the different routes. I don’t think my brain is big enough to comprehend something like that without it cramping all over…
Also Ushio is adorable but I wanted to see her more ! 
