I haven't played the game and I haven't seen the previous anime adaptation, so KyoAni's Clannad is my only experience with the story.
The two season's were very heavily interlinked with one another, I felt the first season was absolutely unable to stand alone, perhaps the whole story should have been one big season. I guess the only reason why they divided it is because the game was divided into the main Clannad storyline and then into an "after story," and perhaps its easier to finance good animation when its divided into smaller parts.
I gotta say Fuuko gets way too much airtime in general, she's so much better in small doses.
Overall I wasn't displeased with the last episode, but it would have given me so much more hope if Tomoya could have found his happiness as a single parent family. I know the premise of Clannad is completely about families and how great they are, but I felt a little jipped at how picture perfect Tomoya and Nagisa's family ended up as. Tomoya and Nagisa from the start were such a strong, stable, and always passionately in love couple, already something that not everyone can have (but it does happen in real life, I know this for a fact) With Ushio they're just the perfect family. Even individually, each of them are perfectly carved into the roles of being a husband/wife/father/husband/daughter/woman.
The most moving moments in Clannad for me were those between Ushio and Tomoya. I became very interested in that father-daughter relationship. Looking at some of the in-between moments in that last ep where there isn't much going on, just a sort of montage of special effects, I think a significant portion of Clannad must feel ridiculous or silly to those who didn't super-connect with the leading characters. Those nothing-happening moments are supposed to be quiet parts of the episode where the viewer reflects on the feelings their characters are probably going through due to the latest turns and all of the events that have unfolded in the whole series.
The time travel, which I was somewhat spoiled for and which I knew had to happen to obtain the picturesque-perfect-family which I knew Key would go for, sadly undo-ed all of my most moving moments from Clannad. I don't feel particularly bad about that but I wish it could have gone differently.
Overall a great anime though, and another Kyoto Animation success story as far as I'm concerned.
If I were in Tomoya's shoes, had found someone I was determined to spend the rest of my life with and lost them after a some years, it would be so difficult to find happiness after it.