Clannad After Story is truly a masterpiece in basically every sense of the word, and I'll be backing that up in the following paragraphs. While I'll be the first to admit the arc concerning Sunohara is a small blemish on the overall piece, I think the meat of After Story (graduation forward) is the part that should be hyper-focused on. Perhaps that's a bit unfair, but it is the section of the anime that takes up the majority of the time and is also the main focus of the entire thing.
Characters
Tomoya
Clannad is not a complicated show. Well... mostly. The plot outside of the "other world" is rather straightforward and true to the spirit of the typical slice of life. This by itself is not a problem, all it means is that the show must now focus on the characters within it. After Story is mainly focused on Okazaki Tomoya, though characters like his father, Nagisa, and Nagisa's parents must also not be ignored. Clannad had a way of doing things that most anime tend to stray away from. Usually, the protagonist is someone who has some specific goal or trait that makes them stand out amongst the crowd, but honestly, Tomoya just started as some dude with family issues, who was bored and entertained himself through his interactions with Nagisa. After Story decides to keep going down this route as it tells his story. Tomoya is still just some dude with issues, but that's what makes him great. The anime doesn't shy away from showing the struggles of life. Sometimes life is hard, sometimes life is beautiful, that's the basis of his growth. As Tomoya learns how harsh the world of adulthood is, he begins to change. He was someone who could usually contain his emotions, but as time went on, it got harder to do so. Nagisa being unable to graduate was an upsetting thing, small but it adds up. His job is difficult and stressful, but it gets the bills paid. His father becomes the talk of the small town after getting arrested for drug possession, leading to the loss of a big job offer. He's slowly being broken, but his marriage with Nagisa helps to pick him up, only for her unfortunate death later to turn him into what he hates the most, his father. It was one of the moments that broke me the most, watching a character I came to care so much about neglecting the responsibilities of being a father and shunning away his kid, sticking her with Nagisa's parents. Going on the trip is what sets him back on the right track, and it was ultimately the meeting with his grandmother that was the ultimate turning point in his mindset, and a big blow to the viewer as well. Tomoya wasn't just as bad as his father, in some aspects he was even worse. Grandma Okazaki telling Tomoya about the big difference between him and his father is something that will get me every time. At least his father tried to be there, even if things ended up falling apart between them. With this realization in mind, Tomoya can secure a new bond with Ushio and finally reconcile with his father. His final piece of growth comes when Ushio also passes on due to the mystery sickness and he nearly uses his wish (to be explained later) to make it so that he never met Nagisa, as then she never would have given birth, leading to neither of Nagisa or Ushio needing to feel that pain. Luckily he is convinced before committing to the wish that he shouldn't have regrets about meeting Nagisa. His story ends with him being able to live a happy family life as his wish grants him a second chance with Nagisa and Ushio both surviving. Beauty through simplicity, Tomoya is a straightforward character done to perfection and he is the foundation that makes this anime so great.
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Nagisa
I think one of the most common criticisms I've seen of After Story is that Nagisa is a bland character and I think that's far from the truth. She isn't the most unique character ever, but she's far from dull. She's someone who deeply cares for those around her and goes to great lengths to keep everyone else in mind despite being in a rough situation herself. Despite her fragility, she wants to support everyone however she can. Tomoya likely could have supported the family on his own due to their small apartment, but Nagisa herself went to get employed to lighten the burden even just a little bit more to show her dedication to Tomoya. To her demise as well, she decided that despite the medical risks that come with her having a child, she would go through with the pregnancy regardless. She's simple, naive, and overall not a deep character, but she doesn't need to be. She plays the role of Tomoya's support beam perfectly, and her loss is what sets Tomoya on his journey to heal himself completely.
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All of the Parents
Sanae and Akio Furukawa are both much different in comparison to Naoyuki (Tomoya's father), but they all share one common aspect in that they will push themselves to help their kids. Naoyuki ended up failing in the end as he didn't have anyone to lean on, but Akio and Sanae are a different story. Their dedication to Nagisa already shown in the first season was great, but it goes even further in After Story. They don't want to lose her in any capacity. Tomoya had to prove himself to Akio to officially marry Nagisa, and once Nagisa passed on, they willingly took in Ushio as Tomoya was starting his most important character arc, while Sanae and Akio finished theirs. The two did their best to the bitter end, and after Ushio was taken back in by Tomoya, they finally had to face the reality that their job as parents was finished as they cried with each other. Naoyuki I'd say I already covered a bit in Tomoya's section, but I'd say his journey starts with the loss of his partner, obviously. That leads to his desperate bid to raise Tomoya, which he ends up on the generally failing end of as his relationship with him deteriorates into practically nothing as the two barely know how to even speak to one another. Luckily all is well once Tomoya realizes that despite the issues they had, he needs to reconnect.
#Art
The anime was done by KyoAni so it's no surprise to anyone that the art for this anime is absolutely stunning, especially for the time it was made. I also shouldn't have to say this, but having a more "moe" style does not automatically make the art garbage. Welcome to anime created before 2010. The general art does everything it needs and I have no reason to dock the anime for it.
The OST for Clannad is probably one of my favorites in anime. It sets the mood for any scene and knows how to keep you involved. In scenes where characters are simply interacting, the music is a more jolly tune to keep you engaged, and somber tones are used in serious scenes where the anime has your attention regardless. If you haven't, I highly suggest listening to any instrumental version of Dango Daikazoku.
#Entertainment Value
Boring is not a criticism. I don't have much else to add here. This is not an anime where you'll have a nuke explode every episode so if you are not the type of person to enjoy a slice of life drama focused on the growth of characters instead of eye-candy fights, I can't say I suggest watching things like this. If you find something boring, that's a valid opinion, but that doesn't make what you watched a bad piece of media.
#True Emotion
The thing that this anime did better than anything I've ever watched was get me to actually care. I don't cry often when watching anime, but you can bet this one had the waterworks going. You want these characters you've spent countless episodes with to succeed and when they hit a bump in the road it hurts a lot, but it isn't just the deaths and sadness that cause tears. While I cried for quite literally an entire episode due to a bunch of small moments following Nagisa's death as Tomoya turned into his father, the moment that impacted me the most and got the most tears out of me was the flower field scene where Ushio is able to cry in her father's arms for the first time since being born. I'll never get beyond that moment without crying like a baby myself. I've seen people call this anime a melodrama, but it's the furthest thing from it. Just because something sad happens, doesn't mean it's trying to be overly dramatic, especially if it's earned the emotion.
#Conclusion
Overall, After Story is what I consider to be one of the best, if not THE best, anime I've ever watched. While the beginning episodes are not particularly relevant, I believe the highs of this anime triumph all else in the end. If there was anything I could forget entirely so that I could experience it again for the first time, it would be Clannad After Story.