The finale post explains the defects (and then repeats the theme a few times):

Of course, as the season finale, there was a lot left to be desired, so I’ll get my gripes out of the way first, namely: the whole rushrushrush feeling that resulted in whisking Shu-Shu out of the way with uncle kiraboshi and the snake on a plane; having the nunnery tarp’ed up and about to be demolished one moment then not (and for the most arbitrary of reasons) the next; and finally the out-of-the-blue fashion show starring the blink-and-you’ll-miss-her-former-appearance-in-the-series afro otaku model. [..]

There was so much to like about this series and while it ended in a decent manner I was exasperated by the lack of a second season announcement or a more definitive end. If only it were 13 eps instead of 11 it probably would have ended a lot better.

This is going to sound bitter, but even my limited expectations about how the series would end were disappointed. I had figured that at a minimum there would be some sort of Shu-centric deus ex machina ending and that the shipping wars would be left in an ambiguous state. But the deus ex machina was one of the lamest I’ve seen in some time. First the blue tarps went away for just about no reason, and then Chieko’s mom just walks in and says she decided not to sell the building. That’s it? No drama? No payoff for any of the work anyone did to save the Amamizukan? Really? I wasn’t expecting the best ending ever given that there was only one episode to do it with, but give me SOMETHING!

In the end, the most wonderful anime of the season floundered at pacing and planning, possibly aided by scheduling uncertainty during the production. And the win was so close.