The biggest question I have for most things is "how."
Okay. At the end of the TV series, Madoka forms a contract with Kyubey by wishing to personally destroy every witch to ever come into existence the instant it's born. This has the side effect of turning Madoka into an omnipotent, omnipresent being since that's the only way that wish could be possible. In the context of the show, it makes perfect sense that she would be able to make that kind of wish since it's established that a person with greater value to the world as a whole can make greater wishes and therefore become a greater magical girl, and thanks to Homura's constant screwing around with the timeline for Madoka's sake, Madoka basically becomes the most important person in the universe. So Madoka becomes a god and uses that power to rewrite the rules of the universe. Fine so far.
Then Rebellion comes along, Homura becomes a witch, Madoka comes to end her suffering, and Homura pretty much rips Madoka out of her higher existence and rewrites the rules of the universe again, essentially putting herself in charge of her ideal world.
HOW.
Madoka was a GOD, on a totally different plane of existence, and Homura rewrites the reality Madoka established more or less because she feels like it. How did Homura get that kind of power, especially without using a contract with Kyubey to get it? "Love" isn't a sufficient answer (not to mention saying Homura "loves" Madoka is questionable at best at this point, and if I get into how disappointed I am in that Homura's relationship to Madoka went from sweet, selfless, and devotional in the TV series to creepy, obsessive, possessive in the movie, I'll really get sidetracked (though I guess it makes sense as far as "the greater the magic girl, the more terrible the witch.")) How did Homura even physically interact with Madoka, anyway? Like I keep saying, higher plane, this was made very clear in the show, nobody should have been able to interact with Madoka and vice versa. For that matter, how did Madoka take on a physical form inside Homura's labyrinth? If she was able to do that, why wouldn't she have done so to see her friends? Does being a god just sort of go away because you forget about it? How did Kyubey go from not even knowing about Madoka at the end of the series (it even flat-out admits there isn't any way to prove Madoka exists) to building a forcefield that can TRAP A GOD INSIDE a short time later?
And now to mix it up a bit with some "whys." Why is Sayaka alive again at the end of the movie? Why can she summon her witch form to fight for her? Are witches like Stands now? And I can understand Godoka enlisting Sayaka's help to get Homura out of her labyrinth, but why in the hell, out of all the other dead magical girls, did she decide to call on the one that most recently murdered Mami? (I know the real reason; fans love Charlotte, but that's not what I mean.)
Basically it felt like the movie was trying way too hard to pander to the fans and be crazy; too many questions left unanswered and half the cast may as well have not even been there for all they contributed to the plot, this was 95% Homura's story. The TV series ending was bittersweet but felt like something was really accomplished, especially as far as Madoka's character development, which was really lacking for most of the show. The movie kind of spits on Madoka's sacrifice and puts her back to being not so much an important character herself as a prize for Homura and Kyubey to fight over.
Uh, I did like that scene where Sayaka talked to Kyoko about having regrets, though. That was really cute.
Does that mean the movie was kinda mediocre, but you love the Puella Magi series too much too outwardly hate it? If so, I feel your pain... 
When it's not exactly a TERRIBLE film, but it just doesn't do the series justice.
