As much as I preferred this movie over the TV series, this is the one thing in the PMMM franchise that even its fans admit had problems. Quite a number of problems. From the very fact that it's a sequel to an already conclusive TV series.
1 ) The first half hour.The whole witch barrier world thing is probably the second most polarizing thing about the movie. By this point in the Madoka franchise's life time you already know what kind of series it is. No one's going to buy the idea that these characters could ever be in a happy and normal world, especially when the trailers show things like Mami and Homura's fight or Homura holding a gun to her head.
We already know that this ridiculous world is fake, we just don't know exactly how. So either you're enjoying the fanservice of watching these characters get along in a happy world, or you're waiting for the story to actually kick in. It spends way too much time meandering around this silly idea that people refer to as some kind of imitation of traditional magical girl shows.
2 ) Too much information withholding.Much like the TV series, the movie relies heavily on characters dancing around each other with information and hiding it until the most dramatic moment possible. In the case of Homura it's understandable because the movie highlights her flaws: That she's unable to communicate with others or rely on them, and that she's too irrational to realize that a witch wouldn't just trap them all in a fantasy world.
But with characters like Sayaka, and especially Nagisa, there's no excuse. Did they need to wait until Homura realized what was going on of her own accord in order to explain everything to her? Why couldn't Nagisa have just changed back when Homura was attacking her and explained everything? Why did she wait until the point that she did to explain what we the audience don't get to hear because they're setting up another DRAMATIC REAVEAL! ?
3 ) Lack of substance.Par for the course in a movie that exists as 40% fandom pandering, there's so much stuff that is just thrown into the movie without any kind of weight behind it. Kyouko and Sayaka holding hands and talking about how Sayaka's one regret is leaving Kyouko is great for the shippers, but consider we saw almost nothing of their friendship prior to Sayaka's death, it feels hollow.
Same goes for that fight between Mami and Homura. There's no emotion behind it. Aside from the simple fact that Homura was trying to attack Bebe, there's nothing that really drives either character into such an intense conflict. It's just a fancy display for the audience. At least the fight against Homura's witch form had more meaning behind it.
4 ) Lack of explanation.Most of the time Rebellion Story is pretty easy to follow, but when we get to the end, things get a little crazy. I watched the entire thing, and I still feel like I'm lost on a lot of things.
All of tumblr's PMMM fandom: Durhur you missed the point! Did you even watch the same movie?
The biggest example is all about the twist at the end. The movie doesn't really make it clear HOW Madoka, Nagisa and Sayaka appear in the real world when at least the former is supposed to not be able to exist. HOW Homura is able to physically handle this non-existent concept, and what exactly happened to Homura's Soul Gem. Those things being corrupted by "love" as Homura puts it is something they've never been established as possible, not to mention this apparently allows her to hijack Madoka's ultimate powers?
And what exactly did she do? We see Madoka get separated between human and ultimate forms for a second and then fancy effects!
And of course there are so many other things that just go unexplained, like what the role of megucas in this new world is, what Kyubey's role is, and so on. I get that it's left intentionally vague to make room for a sequel, but that in of itself is just bad writing.
5 ) The ENDINGYou all saw this one coming. I've already mentioned
in a previous thread how I believe that Homura's actions were a result of a huge misunderstanding between her and Madoka. How Madoka did not have the memories and experiences to make such a powerful, self-sacrificing wish willingly. And how the way Homura words her "dream" leads Madoka to believe that she would be completely detached from those she cares about.
Tying into pretty much all of the above this ending comes together to slap the viewers in the face and say "how will this mess get fixed? Keep watching and find out!"
It's very clear that this world is not entirely a good thing. It was made with somewhat good intentions, sure, but if this world of Homura's was a good thing, then the ending would have been perfectly conclusive, Madoka wouldn't have to be essentially imprisoned in this world, and we'd know what the heck is going on with the law of cycles.
I could also talk about how the movie "ruins the TV show's ending" but that's for the PMMM fans to determine.