It completely failed at trying to tell a conherent story. It clearly strayed to far from comfortable territory, meandering along until realising that they had to draw the show to a (hasty) close.
Personally I don't care if it was retreading the same path as Kanon and Air, in part because I watched Clannad before either of them, but also because I have much more tolerance for unoriginality than a lot of people. It's how well a story is told, how moving they make it, that matters to me more than trying to be original.
Hopefully you're right about the After Story, because I found the ending to Clannad extremely disappointing and don't want my good memories of this show tarnished by the mediocrity that made up most of its second half.