I agree with animus, most of the story arcs in season 1 involved tragedy of some sort. Tomoya was a victim of domestic abuse with a permanent injury to show for it, Nagisa couldn't finish a school term because of her illness and was all alone at school, Fuuko was an astral projection of a girl in a coma, Kotomi's parents died tragically when she was a little kid, etc. The big difference was during season 1 most characters were shielding away their issues since all that stuff had happened in the past. Plus, as the characters pasts were unraveled in season 1 there was lots of comedy mixed in from the supporting cast to dampen the effect of the individual focus characters drama.

Still, for people who prefer everything to work out like in a Dr. Seuss book or a Disney movie I can see how After Story would seem like a poor sequel.