What distinguish Madoka from... was its emphasis on plot rather than story:

>This is where I connect the idea that a big separator for Robinson Crusoe is its emphasis on plot over story. I use these words in the way literary theorist E.M. Forster describes them, and I certainly can't put it any better than he did:
>We have defined a story as a narrative of events arranged in their time-sequence. A plot is also a narrative of events, the emphasis falling on causality. ‘The king died and then the queen died,’ is a story. ‘The king died, and then the queen died of grief,’ is a plot. The time sequence is preserved, but the sense of causality overshadows it. Consider the death of the queen. If it is in a story we say ‘and then?’ If it is in a plot we ask ‘why?’

Madoka saw all that was wrong with Magical Girls but still believe it can be right.  In Rebellion, Homura sees all that's right with the new system, but believes it's all wrong.