I guess I will weigh-in right now while the topic is relevant. I'd prefer to wait until I can marathon s1 and s2 and really sit down and think about the series but that won't be happening until Summer and exams are over. So I'll give my impression of the series after watching it on a weekly basis and save a more thorough post for later.
First off, it is very, very hard for me to pinpoint an exact rating for Clannad. I guess sort of like Tomoya's story, this show has been ecstasy at times and then a bit "unejoyable" at times. Like others have said, the mini arcs at the start and the discombobulated ending marred the overall rating I would have given it. But unlike others who have said the same, the overall rating I probably would have given the show if it were perfect would be far and away over a 10, because I love this kind of a series and I loved the middle. So it's hard for me to give it a rating, because does it still get a 10 despite obvious flaws? Something with obvious flaws shouldn't get a 10, I think...
Ideally, I think a 10 should be given to a series that at least keeps your attention from the start(it can be a little slow for ~3 episodes), but eventually it should draw you in(the sooner the better) and keep your utmost attention all the way to the very end. And the ending should leave you feeling like you spent your time watching something that was clever or poignant and intelligently made. Air and Kanon, season1, all fit the bill, After Story did not though. Yet, I know that I enjoyed some of the parts from After Story more than anything I've seen in Air or Kanon or even season 1 which I would all give 10's to. So those more powerful scenes have to account for something.
I believe that every episode needs to be relevant to the overall story, in some way. I don't mean that there should be no filler scenes or mini-arcs. Such episodes can work, even if it's just a couple scenes during the filler episode where series' tones and themes are accentuated in those few scenes. In the case of Clannad doing it the right way, it was Tomoya singing to his Daughter or him crying over the loss of Nagisa, or creating some interest in the hospital with Ushio mysteriously visiting it. Something as small as that makes an episode relevant to me. It drives the moral of the story home a little closer. But, I don't want any complete throw away episodes. The first ~8 episodes I felt were just about throw-aways(I will have to watch again to confirm this). I suppose the themes were intended to drive home the theme of family more, but those arcs were just too weak for me. They felt like completely different side-stories that had little consequence to the main themes.
I think the difference between the mini-arcs and the main arcs for side characters, like Fuuko, is that Fuuko's arc stays vivid in my mind even after her arc is done(from season 1 no less) I thnk that really contributes to an understanding of what Clannad is about. Forgettable mini-arcs don't do anything for me(I suppose whether they are memorable or not is up to the viewer, so maybe these arcs are powerful, "Relevant" for some.) Also, I like for any of the characters that were focused on to still stay relevant to the characters that the story is currently focusing on. I like for side-characters to be re-visited and to get updates on them. I like that Fuuko is a relevant part of the overall story even after her arc has ended. (On the other hand maybe I wouldn't want another episode with 5 minutes of Misae, Sunohara, and all of the side-characters either. So I think in After Story's case they just threw in too many arcs, when I would have preferred more focus on the main story.)
As for the ending, I prefer to save the climax for the ending, it feels like the climax of the story was in the middle, and everything after was downhill. There needs to be another, preferrably greater climax at the end. What they gave us at the end, did not feel like a climax to the themes of the story thus-far and all that happened up until the final episode. I would have preferred another episode or two at the end to really put-together what the ending theme of the story is about after all that's happened, that bringing happiness to people is what the story is about now, living life the way it's meant to be lived, not doubting your decisions for a second concerning the one's you love. They should have built up to that climax some more, because the way it's done, is that it's just sort of thrown in there, it's a vague message they're sending. I want a powerful message that will move me. It just doesn't have the proper build-up that the main theme of a story of this caliber deserves. If it is an important theme, which it should be since it's supposed to be their climax, the final theme of the show which should be the lasting theme of the show, should be built up just as well as episode 18. With two episodes showing Ushio & Tomoya's relationship. The ending should have just as much build-up, there should be two episodes showing the relationship between Tomoya and the miracle.
The beginning with the mini-arcs and the ending are such glaring flaws it's very hard to give the series a 10. But, thinking about it, this thread is about considering the series overall, and I think when it all comes down to it, that the middle arc is so memorable and powerful that it makes it worth watching over anything else so far this last year IMO. It is strange to give something a "perfect score" when it obviously has flaws, but I would say that this show is definitely a must-see show more so than say Kanon, which I gave a 10 to(Which was enjoyable from start to finish and had some amazing story arcs IMO). But since I would have to give the nod to Clannad, when comparing the two, I think I would by default have to give After Story a 10, because it's better than some stories that I've already given a 10 to.
Overall, great show. So now I'll just throw in some thoughts on the technical aspects and spout out some other ramblings: Tomoya, Ushio, Tomoya's Grandmother had perfect voice acting for that dramatic episode. One could not hope for better voice actors for serious roles IMO. I hope they'll appear in drama series' again in the future. The Furukawa's, and Fuuko, they had perfect voices for a feel good story and for bits of comedy(Well I already knew that about Kikuko Inoue). I hope Ai Nonaka will get a main role in a comedy(Bigger than the one she has in Zetsubou) On the whole I could not envision better voice actors for the series, at least for the main roles.
Music, is always spot on with the animation, that is truly an art in itself to get the scenes to match up with the music. The way distant years starts off somber and sad as Tomoya recollects about the harsh past he spent with his father, and the way as soon as Tomoya becomes resolute about how to think about his Father, the music picks up, and he says "iie" or no in response to whether his father was a bad father. The turning point in the characters way of thinking is exactly on key with the turning point in the music. Perfect directing by all of the staff for that episode.
Animation was a bit off though throughout the series, it was inconsistent. This is just conjecture, but I think they have two studios working on the animation. Their main studio, Studio Blue? worked on the important episodes and their child animation studio, Studio Do seemed to get the episodes that were less important to the main arc...
In summary, they upped the ante with Clannad: After Story, they ended up jumbling and botching a few parts here and there, which is the first time I've seen KyoAni make a mistake in my eyes(Seeing torch was when doubt first crept in, I said so in the music section when the first episode came out.) But in the end I gotta give Clannad a 10, the story just soared too high there in the middle to not give it a 10. However, because of the errors that I saw, from now on I'll once again be a bit apprehensive in the future products from this studio. Just when I thought I could take the work coming out of KyoAni for granted as being just about perfect too...(K-on! already seems a bit rocky and ordinary man
IMO). But as far as Clannad goes, I must just say: Bravo Clannad!, you had me hooked from the first episode of season 1 all the way to the end of After Story, I will always treasure the memories of the characters and the story.
Really? And here I thought it was because of the "magical reset" that seems to be popular. Oh wait...that is the ending 
