I've watched the Madoka movie several times now, and I like it. I'm certain of that much. I'm almost certain it hangs together, that there's sufficient internal logic to justify everything. I still haven't figured out certain things, and it bothers me.
But I'm also conscious of the fact that I hold Madoka to a much higher standard than most anime. I expect its iconography to be precise, with a clear and lucent correspondence between sign and signified. There are objects that the third movie imbues with significance, and I think that if I could figure out what those objects meant, I'd be much closer to figuring out the entire edifice.
It's not something that I worry about, with, say, Eva. I demand a certain amount of rigor from Eva, but it's more in the matter of characterization than symbolism. I don't worry about what the dead sea scrolls say, because they're background. Atmosphere.
In terms of symbolic nicety, the closest thing I can think of is, again, Utena. Not everything has meaning in Utena, but the things surrounding the core of the story -- the background at the student council meetings, the duels, the things they say to justify themselves -- these are measured, and freighted, and in the end weighty enough to be satisfying.
So it is with Madoka. And if I haven't gotten all the loose ends tied up yet, I'm satisfied that they can
be resolved, and that's really enough for me. Highly recommended.