They could have took the realistic route a la KgNE but it's all due to the VN it was adapted from I guess.

Having not played it I would like to know if there was an imperfect but still good ending in  Nagisa's route.

Edit: MAJOR SPOILERS - Looks like an animated version of a realistic conclusion exists - the film. Might check it out now..

But Kanon and Clannad follow the same kind of "special" ending formula so I guess it is a Key thing. To be perfectly honest the very end of After Story didn't sit as well with me as Kanon's ending did - it came across all a bit too surreal but I considered the overall content of the series, from beginning to end to decide on its rating. I definitely consider it significantly superior to most of the anime I've seen, which is what earned it the 10 I gave it on my list - despite my honesty admitting its imperfection too - but that's the only way I can make it stand out from the 9s which I don't consider to be as good as Clannad. Perhaps I should downgrade everything to reflect this. It's worth mentioning that I don't have an issue with its indulgent side either so its probably that side to it that worked with me better than yourself. Glad to hear you enjoyed it though.