Thrilling plot, surprising character development (especially Homura, although not unpredictable), epic music/sound arrangement, beautiful artworks (my favorite SHAFT style that gives nebulous emotion), and the crucial point: the familiarly twisted and philosophical story written by our Urobutcher that cast doubt on common humanly moral quality, MSMM has the essence of a masterpiece.
The problem is the weak directing (mostly our main character Madoka, too common and the typically weak-minded main character, even though she's a girl).
And the biggest minus blames on the stupid Science demonstration (same problem occurs with Steins;Gate, but S;G is the kind of "intricately incorrect" (therefore watchers don't understand anything at all -> they thinks "it is true" easier); MSMM's is not complicated enough for normal watchers because it is both wrong and simple to understand so everybody knows that it is wrong. (The prejudice of knowing that this is false make watchers think that this movie is spreading bullsh*ts -> lower rating)