I think our disconnect lies in the fact that you think something's a plot-hole if a character didn't make a perfectly logical, rational decision at every turn. I think realistic characters are flawed ones. In fact, it's made pretty obvious that there's a constant tug-of-war because Kyubey's cold rationality and the irrational nature of the human spirit.

Sayaka's arc represents the misplaced sense of self-righteousness that humans have when wanting to do good. A selfish wish would've been totally out of character for her. She wasn't a selfish person; she was a selfless person with underlying selfish motives. She thought she could gain satisfaction by pleasing other people, but she only got unrequited gratitude. Her character goes right along with the theme of moral ambiguity and the belief that no action is either pure or impure, selfish or unselfish, just or unjust.

Other than that, I think the only thing you have wrong is your view on what a protagonist is, and what your view on narrative is.

A protagonist isn't necessarily a main character or the point of view from which the story is being told. The protagonist drives the action in the story. Though the story is told mostly from Madoka's point of view, the hero/anti-hero/protagonist driving the plot forward is Homura. That's really the opposite of lazy writing. Any writer could've told the story from Homura's point of view, but from Madoka's we see just how cruel and uncaring the universe can be when you act nobly, whereas in a typical vanilla story you see a hero being rewarded for his good deeds. That may not be the most complex theme, but it's an important underrepresented one.

And I'm going to have to disagree still that Ep. 10 was "exposition." It was part of a non-chronological narrative, but that's still a narrative. Like Bebop, the entire show can be viewed as an epilogue to a much longer story, where we're only given small glimpses of a character's past, his development, and his motives. Saying Ep. 10 of PMMM would be like saying Ep. 10 of The Tatami Galaxy was exposition, and that Watashi's character growth didn't count because it happened outside of time and space from a reflection of all his past lives. I just think you're not used to non-chronological narratives.