The fight between Mami and Homura: a duel between two of the most badass characters in the entire series, both gunslingers and both extremely capable of Gun Fu.
You forgot about one thing which is even more awesome : The entire time, Homura wasn't fighting the real Mami but a perfect copy of her, made from ribbons! Mami fought Homura to a standstill without being in any danger.
Sayaka predicting Homura was about to use her time shield and jamming its gears shut with her sword.
Sayaka head-tilts toward the screen, a shocked look on her face. Madoka, normal Madoka, is reflected in shadows in her eye, framed against a starry background. Then...BOOM. Ultimate Madoka, her massive wings unfurling from her back and Rapunzel Hair blowing in the wind.
Even though it was an awful thing, the Incubators get some awesomeness credit for their Isolation Field. To explain, Madoka wished to destroy every witch before they were born, in all times and worlds, with her own hands. And the Incubators found a way to block it. (Of course Madoka beat them in the end, but still.)
You also have to give them credit for the guts and the scope of their whole plan. Sure, the end goal is horrible, but you can't help but have some admiration for the fact that the Incubators intend to bind a Goddess to their will and subvert her to their own ends. And even though it did end up backfiring horribly on them, the cold logical way Incubators approach things suggests that they probably had some evidence leading them to believe that they could actually do it.
The battle between Homulilly and the magical girls. Madoka can't use her full powers with Kyubey watching...so Sayaka and Nagisa reveal themselves to be part of the Law of Cycles and summon an army of familiars to fight Homulilly's own army of familiars. Sayaka further summons Oktavia von Seckendorff to hold off Homulilly while Nagisa and Madoka attack the ceiling of Homulilly's barrier. We also get to see things like Oktavia wielding Kyouko's spear and Mami using a cake tank on rails to deliver the mother of all Tiro Finales. Once they break through the barrier to reveal Kyubey's isolation field, Madoka reaches to out to Homura's remaining humanity and they deliver one final shot that punches straight through the isolation field and launches a Rain of Arrows on the flabbergasted Incubators watching from outside. It's one of the most epic fights in the entire franchise.
Another awesome but horrible thing. You know how Kyubey tried to observe the Law of Cycles so they could interfere with it? That's what Homura did. In fact, it's suggested that this is how she gained her new powers.
Homura essentially putting down Kyubey after the credits. It really underlines how Homura is in control of the new universe, with the Incubators' efforts now benefiting her. Though there are implications of Homura taking over Madokami's role and taking Madoka's power and memories from her for an admittedly selfish purpose.
This isn't just a great moment from the movie. This is perhaps the greatest Awesome Moment in the entire series. Say what you will, but one thing cannot be denied: for the first time in trillions of years, millions of innocent girls from thousands of planets, a TV show, four Manga, three movies, a video game, and COUNTLESS time loops, the unthinkable FINALLY happened. Kyubey LOST. Until this point, he either straight-up won or walked away relatively unscathed, even if he hadn't gotten precisely what he wanted. But this time, the little fiend not only walked away with nothing, he and the rest of the incubators end up Homura's slaves. Say what you will about Homura by this point, but the fact remains she finally, finally, FINALLY beat him outright. And best part is that just like last time, he has nobody to blame for it but himself.
Sayaka with control over Oktavia as Summon Magic. Weren't we all hoping that would happen in the series? And the Witch itself is a juggernaut of destruction.
On a meta example, the movie itself being submitted for the Oscars, something that even Rebuild has yet to achieve. Granted, it was only a submission, but this would make it the first movie of an anime in being considered for the award at all. Many are praying to Madokami or Homucifer for the movie to be one of the finalists.
Sadly, subverted when it failed to make finals. Supposedly, the judges didn'teven watch it. Looks like we'll need Homucifer after all.