Air is really a great anime. When I watched it, I felt very depressing. For maybe, the 3 last episodes, I was always crying ! The end was also really shocking for me, who thought like you, Kanon, that Misuzu would escape her fate like always... But, she didn't.
Like you, I thought her act was really great but the 2 others arcs was not really good. At the end of them, I didn't understand quite what happens with them. Particularly, the little girl with the dog, who stays in the city after her arc, but we don't know what happen to her. I was really disappointed.
But after all, Air was for long time, my 2nd place in my top 10 anime.