Madoka's flip-flop on whether or not she would sacrifice herself as she did at the end of the original series seems a bit strange. Then you realize that this is Madoka without the psychological torment she sustained during the anime that drove her into a corner, and it makes a bit more sense.
With all the Fan Works and Licensed Games and other Spin-Offs, it's easy to forget that the beginning of Rebellion is actually the first animated appearance of all five magical girls fighting together. It's a big deal for a reason.
While the level of seriousness varies, every entry in the Cake Song means something to the character singing.
Sayaka is a raspberry as a nod to Cure Berry and their matching elements.
Kyouko is an apple because it is now her Trademark Favorite Food with boosted significance from The Different Story.
Mami is cheese, Bebe's favorite food. Bebe likes Mami, too, and has eaten her in another timeline.
Homura says she's a pumpkin. A story surrounding the pumpkin involves the origin of the Jack-O-Lantern, in which a man was able to prevent the Devil from claiming his soul by asking him to fulfill a last request, only to trap him with a crucifix. He could neither go to Heaven or Hell afterward. Some fans have pointed out the Dark Orb's shape resembles a pumpkin.
Alternatively, Homura's a pumpkin because she's really a witch.
Madoka says that she's a melon, split to bring sweet dreams. Now, what happens in the ending of the movie? Madoka is split from Madokami and forced to return to her human form, though there is still an uneven connection to her goddess powers.
At the end of the movie, from Madoka's power, a 'sweet dream' - Homura's new world, in which everyone is happy was truly created...
The line they each use to describe the cake and pass the song onto the next singer is equally significant:
Bebe starts with "Is the cake Sayaka?" Bebe is Nagisa; she and Sayaka are the only ones who actually know what's going on because they're agents of Madokami. No one can understand what Bebe says, but Sayaka picks it up easily nonetheless.
Sayaka passes with "The cake is red" to Kyouko, whose theme color is, obviously, red.
Kyoyko passes with "The cake loves Bebe" to Mami. Apart from just being true in general, Mami really does care about Bebe, and she and Homura come to blows over it later on.
Mami passes with "The cake goes around in circles" to Homura. She has no reason to know that. As far as Mami ought to know, there's only ever been one timeline; this is a hint that Mami's memories have been manipulated by Homura, because only Homura would know about her time-looping.
And Homura passes with "The cake is sweet" to Madoka. D'aww. None of the other girls should know anything about Madoka at all, so having anyone but Homura pass the song to her would crack the illusion.
One of the last lines in the song: "on the table/platter is a cat's dream". Homura's barrier is part of a larger scheme by the Incubators to trap Madokami within their Isolation Field, and Kyubey has been likened to a cat...
We later see Homura's body laid out on a funeral altar. She's literally on the table and, as the only magical girl capable of proving the existence of Madoka, she's a dream-come-true for the Incubators who want a bigger energy yield.
Speaking of the song, that scene seems to echo back to Episode 3 of the anime, and especially to the first movie's rendition thereof: a bunch of girls sing a cute-yet-disconcerting song about food, then Charlotte proceeds to eat the "food" in question.
The entire scene itself is about as weird and random as it gets, even for a Magical Girl movie. It's one of the first clues that something is amiss in the setting. After all, people usually see weird and random things whenever they are having a dream.
Even the accompanying hand gestures can be interpreted as symbolic, but this time in reverse:
Sayaka covers her face with her hands. Madoka's eyes were metaphorically covered by Homura for most of the series.
Kyoko taps her fingers in a rhythm on the table, as musicians — like Sayaka's crush — are wont to do.
Mami puts her hands together in prayer. Kyoko's wish centered around her father's church.
When it's Homura's turn, the camera pulls away from her and focuses on Kyoko and Sayaka. Mami had less screentime than both of them, only appearing for 3 episodes.
The camera also makes it difficult to see what Madoka is doing, but she also appears to cover her face with her hands. This could be interpreted as Homura's true motive being unknown for most of the series.
Madoka had the power to remake the universe as the raison d'Ítre for countless timelines. She wasn't the only one. All of Madoka's massive karmic potential was just riding Homura's wake.
Equally brilliant is the call-back to the original series (and consequently the previous movie). When Kyubey discusses the reasons behind Madoka's huge magical girl potential, we see a shot of her with her body tied onto various strings, representing Homura's various timelines. When Kyubey pins the blame on Homura, we see the same shot with Homura replacing Madoka. That's a really long-shot foreshadow, if not a downright lucky coincidence.
After the bus scene, the next we see of Kyouko is her in the arcade, in her casual outfit from the series, playing a dance game. This could probably mean that she's quit school and gone back to her old time-wasting habits since she and Homura found out that they're in a fake world, and have had their minds tampered with to fit in.
In this world, Kyouko and Sayaka have formed some sort of relationship. They even live together. The reason Sayaka doesn't make a fuss over Kyouko skipping school is because Sayaka has known that the world is fake to begin with and she realized that Homura and Kyouko have figured it out.
If one pays really close attention to the details in the beginning sequences, its easy to tell its a world of illusion made by Homura. Madoka's hair when down is longer in the movie than in the beginning of the anime, alluding to Madokami. Similarity the classroom was a lot more golden in the movie. When Homura enters, she is confident rather than shy but still her moe self, alluding to the fact that she wants to be confident but not the ultimate protector. On hindsight it gives us a really good insight on Homura's psyche.
At the conclusion of their battle with a Nightmare, the magical girls have to sing to it. They all sit in a circle and sing a cutesy, repetitive song about cake and fruit. It seems completely silly and ridiculous—Madoka isn't a musical!—until you realize it's a lullaby. Only natural that you'd need one to defeat a Nightmare.
The same goes for the first Nightmare fight: while the girls don't sign themselves, the lyrics for the song "Not yet" are very much akin to that of a lullaby.
Remember in episode 6 of the anime when Madoka asks her mother for advice about how to help Sayaka? Junko tells Madoka that doing the right thing doesn't always create a happy ending, and suggests that Madoka do something wrong for Sayaka. Junko also warns that it won't be a neat and tidy resolution, and that Sayaka might misunderstand Madoka's intentions. Now apply this to the ending of Rebellion. Homura believes that Madoka's self-sacrificial ascension is keeping her from being happy, and so she does something wrong - extremely wrong - in order to ensure Madoka's happiness. The resolution is not neat or tidy.
It was mentioned in the earlier season that Sayaka is the only magical girl who dies in every single timeline, either by turning into Witch or by overusing her magic. Even Madokami couldn't do anything with it since then Kyosuke would land back in hospital. Homuniverse is the first timeline ever in which Sayaka is alive and yet Kyosuke's hand is still healed.
At one point Madoka says it's been a month since Homura transferred in. In the anime Homura says she repeats the same month over an over. At the end of the month, Walpurgis Night appears. In other words, Homura's search for the truth is the equivalent of Walpurgis Night's appearance.
Wonder how Homura's witch barrier Lotus-Eater Machine was able to alter the memories of Mami and Kyoko? Go back to episode 4. Remember when Madoka gets sucked into Elly's barrier? She gets caught by Elly's familiars and is then altered. Her body changes to resemble the art-style of the barrier. Morever, Madoka is shown images of Mami's death, which suggests Elly is reading her mind. In fact, Madoka only returns to normal when Sayaka attacks Elly. The implication is that anyone "invited" into a witch's barrier is brought under their power. There's no reason to believe witches can't do this to magical girls...but it's easy to see they wouldn't want to since magical girls can fight back. In Rebellion, when Kyubey is giving his explanation we see scenes of Mami and Kyoko doing ordinary things before Homulilly's Clara Doll familiars appear behind them. The Clara Dolls are powerful enough to take on a magical girl, so they must have been able to overpower Mami and Kyoko and bring them to Homulilly's barrier. Once caught by the barrier Mami and Kyoko were "altered" like Madoka was in Elly's barrier...but the alteration was done to their memories.
Some viewers get the impression that Rebellion betrays the point of the original series. Of course it does! With a movie titled Rebellion, how could anyone expect anything less?
It seems a lot of people were puzzled by the scene when Homura, during her last talk with Sayaka, was showing her hands a lot. She is showing that she doesn't have her contract ring nor the fingernail mark anymore, though she still has her Soul Gem (or whatever it is now) which could be summoned by Homura, as see in The Stinger. During her talk with Sayaka we're shown in a flash her new earring with a tiny purple jewel on it. It could be she can swap places and make the Soul Gem less noticeable as an earring.
Take a good look at the teacup that falls in Homura's new world. Homura isn't dropping it, it's being pushed it out of the way. In fact, she's moving her hand forward, towards where Mami is. Was Homura trying to bother Mami, or was she trying to reach out to her? And then there's the part where she refuses to let her familiars catch Kyoko's apple - as noted below, it's implied the familiars are expressing Homura's true thoughts. Is Homura trying to get Kyoko to waste food, or is she denying her desire for Kyoko's friendship?. One interpretation is that Homura resents them for saving her. Her familiars still represent and play out her self loathing, and she equates herself to the devil because she knows her actions are wrong. She was counting on the two to kill her and cried out against their rescue. Earlier, she confided in Kyoko and flinched over hurting Mami. Her actions are very much intentional, and this is her showing they are no longer on good terms.
Here's something the show doesn't tell you but expects you to figure out yourself. By keeping her from Homura's Soul Gem, Kyubey's Isolation Field was blocking Madoka's omniscience. No wonder she couldn't see the movie's outcome. And even after the Isolation Field is broken, Madoka is still in the form of a human, experiencing time linearly and being unaware of the future.
Madoka wished to erase all witches with her own hands. Now where does Homura grab Madoka?
Wonder why Homura "sent" Madoka to America? Because English was the subject Madoka had the most trouble with.
Pay attention near the end. There's a Pyotr and a bunch of Anthonies in Homura's new world. Obviously they're like Sayaka and Nagisa and are unable to return to the Law of Cycles. This is clearly another part of the Sequel Hook. Heck, during the Homulilly battle we're shown familiars from every single witch seen in the anime...except Walpurgis Night. And one of the girls who became Walpurgis Night still sends the elephant afterwards.
Near the end of the movie, Madoka's wearing yellow ribbons. The ribbons are most likely a reference to the first episode. Madoka almost puts on yellow ribbons instead of her signature red ones before her mother tells her that she looks good in red. And since Homura had her red ribbons this time around it seems that she had to settle for them instead. There's even a small echo to what Junko said after Homura gives them back and tells her that they really do look better on her.
She could also be wearing it in reference to a certain other godlike schoolgirl. This may be a nod to an oddly similar plotline. Spoilers for the Haruhi anime: The omnipotent girl's powers were stolen by a normally logical and dependable friend, who became emotionally unstable after an exceedingly long "Groundhog Day" Loop. The latter used the stolen power to construct a more normal and peaceful world for everyone, even though she knows it probably won't last. Is that the plot of Rebellion, or Disappearance? The pre-movie ending of Madoka Magica is somewhat like the "Haruhi's world" ending of Disappearance, while Rebellion takes the "Yuki's world" and The Vanishing of Nagato Yuki-chan route.
During Madoka and Homura's conversation in the field of flowers, just before Homura turned into a witch, we can see that the states of the flowers practically summed up Homura's entire journey. Why? Because they are manifestations of Homura's psych, and it was at that point that the idea of becoming The Devil first came to her mind, along with the determination to make Madoka happy. The idea only got reinforced after she had become a witch. "No matter what sin I commit and what form I take, it's all right as long you are near me". This is the moment when Homura finally lose it and breaks down. And this is the moment in which Homura decide she will turn into Devil.
Sayaka being an angel and summoning Oktavia references an ending of The Little Mermaid, where the mermaid becomes an air spirit and gets to go into heaven by doing good deeds. Notably Sayaka is working with the childlike Nagisa; the ending of The Little Mermaid indicated the behavior of children affected the amount of time the mermaid had to work to get into heaven.
The classmates having a face in Homulilly's barrier during the redux of the Nakazawa scene might be weird, given that they are latter seen without a face like the rest of the fake city inhabitants. The reason? At the beginning of the movie, Homura isn't suspecting the masquerade yet, once she start having doubts, the first cracks in the illusion appears with the burned out face of the fake inhabitants. That scene is a subtle hint that the barrier is reacting to Homura's state of mind, foreshadowing that she's the witch who created the barrier.
Of course Homura's Soul Gem changes shape: it's a crown. Specifically, it's the king's crown as portrayed in chess symbols; meanwhile, the ordinary soul gem does resemble a pawn somewhat. Thus, it's perfectly fitting for someone stepping up to become the Princess of Darkness.Why does it do that? Because nothing, even Kyubey, can undo a wish already granted. If Homura's Soul Gem really had hatched into a Grief Seed, even the isolation field wouldn't have prevented Ultimate Madoka from reaching her because her wish was to defeat all witches before they're born, period. However, in the new universe, Homura is her same Bad Ass self she was, even though without a Madoka to protect, she has no reason to make the contract, so what did she wish for? She didn't get one. Her contract was part of the old universe and it carried over, only her powers changed to reflect her new purpose. On top of that, her magical potential would be just as strong as Madoka's, for the same reason. In other words, her Soul Gem evolves into a crown and she conquers Kyubey because she granted her own fucking wish."
Kyoko isn't seen using her Rosso Fantasma technique in the movie, even though she's kinder and friendlier, and doesn't show traces of her old sour-natured and cynical personality, the reason is that in the pre-Madokami universe, Kyoko lost that power when her whole family died, years before Homura contracted and began her time loops to save Madoka, so she doesn't know that Kyoko has that power. So Homulily's barrier couldn't include the knowledge of this power when it altered Kyoko's memories, explaining why she still couldn't use it : she literally forgot that she have that power!
Homura usurping Madoka's rule makes a whole lot of sense when you reflect upon her wish. She wished, in its barest bones, was that she'd be Madoka's protector instead of the other way around. Another way of looking at that wish is that she wished to switch roles. It also explains why Madoka is the transfer student instead of Homura.
The Exact Words of Homura's wish make her rewriting Madoka's universe much less of an Ass Pull when thought over from this angle. Sure, Madoka gained godlike powers due to the constant timelines focused on her, but the wish was still made in a timeline Homura created to redo their meeting...Conversely, Madoka's witch possessed the capability to absorb all life within its barrier. By stopping her from purifying her Soul Gem, Homura essentially does the same thing.
To add more Poor Communication Kills points to the flower bed scene: Homura is telling to an amnesiac Madoka that she had a dream about Madoka leaving forever, to a far away place, and that she, Homura, wasn't able to see her anymore. Madoka of course felt bad because she would never do something to make her that sad...but Homura didn't tell her that she did it "in the dream" because it was a necessary thing Madoka needed to do because it would save a lot of people. Maybe Homura unconsciously kept that vital information from Madoka, because she wanted this Madoka, either an illusion or a fake, to sympathize with her and say that she would never leave her, forsaking the world's safety for Madoka's happiness.
In Homura's despair sequence, after she fails in saving Madoka from falling down the chair and explodes into pink milkshake, some viewers may find the creepy Moemura-looking things that look down at an angsty and shocked Homura weird and unnecessary. This is actually a nice metaphor: failing to save Madoka from sacrificing herself, she can't forgive herself. That's why her creepy doubles look down on her: she's accusing herself.
At the beginning of the movie, after Homura's brief soliloquy about Magical Girls and their endless fight, her Soul Gem falls into a open window that symbolizes her potential future salvation by the Law of Cycles, as well-demonstrated by an illustration came bundled with the OST. At the end we see the same window, closed this time. The window is the way to the Law of Cycles (Madoka), but Homura has kidnapped her and stolen her powers; the Law of Cycles is inaccessible now. Note, however, that the window is not locked or barred shut. It's held together by the very same ribbon that, despite its apparent fragility, symbolizes an unspeakable bond of friendship. This implies that Madoka may recover her powers at any time - but to do so, she needs to renounce Homura's friendship forever, making her situation somewhere between "hostage of her own kindness" and "playing along willingly for Homura's sake".
The reason why the Holy Quintet feeds the Nightmare while singing a lullaby-like song, it's because, normally, you have bad dreams if you go to sleep with a empty stomach.
The "Gott ist tott" scene. The original quote says "God is dead, and we have killed him" referring that, if there's a God, humanity has taken away his purpose with science. Homura is angry that the witch that created the barrier is making null Madoka's sacrifice for the Magical Girls' sake for making a world where their fight has no actual purpose. The Clara dolls, the witch's familiars shout that God is dead because their world has taken Madoka's purpose.
An interpretation of the full quote of "God is dead, and we have killed him. Yet his shadow still looms." is that humans didn't take his purpose, they took his power to fulfill that purpose and had nothing to fill the void leads to an interesting bit of alternate interpretation and possible foreshadowing for future continuation.
Take a good look at everyone's transformation sequences. Almost everyone has runes in them somewhere: Mami, Kyouko, and Sayaka's names, Homura's cryptic messages, and Bebe / Nagisa's magical girl recipe. Who is the only one without any runes in her sequence? Madoka.
When Homura kidnaps Madoka, we see her split from her Goddess form. The Law of Cycles still exists in the world because Madoka's wish to defeat all witches before they're born still stands, it's just that in Homura's world, there are no Witches. So what does that leave? Madoka, a goddess, in human, mortal form. Madoka's wish made her God, Homura's wish made her the Devil... and now Madoka, living in Homura's new world and possibly destined to become Homura's enemy, is Christ.
Akuma Homura tells Kyubey that the Incubators are necessary in her new world because something still has to be done with the curses. Then we see him curled up and traumatized, and we know that since he "eats" Grief Seeds and Cubes, he can absorb curse energy. Homura is forcing him to absorb the grief of her new world in order to keep it a happy place.
Homura becoming what is essentially the devil using The Power of Love makes a huge amount of sense when you consider that she basically turned herself into Madoka's opposite. As Madoka became the embodiment of hope because she loved everyone and wanted to make them happy, Homura became the embodiment of love for one's self, prioritizing one's own happiness over everything else. This can also explain why she can only seal Madoka's powers and not fully remove them from Madoka herself. As long as she can keep Madoka's selflessness in check, she can prevent Madoka from accessing her Goddess powers.
There are a lot of instances where fire, or anything alluding to fire, is shown in the movie because the name "Homura" means "flame." Homura also calls herself a demon after taking Madoka's powers, which is quite fitting because demons are mostly associated with fire, or to be more precise, burning Hell.
Even more meaningfully it can also be written as "heart on fire", "village protector", or "stride approaching happiness".
Kyoko is such a Flat Character because everything is happening in Homura's Soul Gem. Homura didn't interact with Kyoko enough to know there's more about Kyoko than her brash personality, Big Eater tendencies, her fondess to Sayaka being big enough to die for her so that's all the personal tracts she could give her in her Witch Barrier. This would also explain why to Homura, Kyoko's character seems strange.
Homura's actions in the end meant she was making just as big a sacrifice with just as big a consequence as Madoka did in the anime. Kyubey got what he wanted: he was able to observe the Law of Cycles and could see exactly how Madoka appeared. As long as he keeps making contracts, he'll have infinite opportunities to experiment with ways around it, which means that the chances of Madoka being destroyed, sealed, or otherwise manipulated jumps to 100%. And that would indeed be the case, if Homura hadn't slapped him down so hard he left cracks in the pavement.
Sayaka says she sympathizes with the witch that created the barrier all of them are trapped in because as a former witch, she knows what it is like to want something so badly that a person falls into despair when he or she fails to attain it. This also foreshadows the fact that she knows that it was Homura who was making the barrier, since out of all of them, she never really got what she wanted, despite being the most dedicated to Madoka's cause.
On the possible answer to the question of why the incubators would choose Homura over other magical girls as their lab rat for their isolation field, one could theorize that since they are already operating in a system bound by the Law of Cycles, so anything made within the system, such as Magical Girl contracts and Soul Gems, would not be a good specimen for their experiment. They probably theorized that Homura, whose magical girl powers did not come from the current system and possesses knowledge of a system they had not known, is somehow connected to the "old" system.
When Homura and Kyoko decided to go to Kazamino city, the reason they cannot get out of Mitakihara city because Homura doesn't know what Kazamino city looks like, most likely because she has never been there. This also explains why the people have strange looking faces once she begins to uncover more of the truth, aside from the people she knows well, everyone is a stranger to her.]]
From a logical standpoint, the incubators' plan of trying to control the Law of Cycles fits perfectly well with their characters as purely logical beings. Their quest for finding more efficient ways of collecting energy mirrors how humans are constantly searching for more efficient energy sources.
Think about why Mami suddenly recalls the wraiths. It's Homura's barrier. Mami remembers the wraiths because Homura wants her to remember.
Sayaka has the ability to summon Octavia, and the familiars of all the defeated witches also participate in the final battle, because of the way the Law of Cycles works. Madoka defeats all the Witches before they're born so they don't exist, so what are they even doing there in the first place? Because Witches still do exist, they're just never released into the real world. When they become part of the Law of Cycles, their witch becomes their Superpowered Evil Side, just without the "evil" part.
Homura's power to create the universe again is fueled by love. Remember that strong emotions are the power source for the magic they give to magical girls, and that hope and despair are considered opposing elements. Madoka's wish created a world out of hope and destroyed a world with despair. Homura's world is the product of Incubator magic, and she doesn't have a loophole like Madoka does. That's why she's hinted to have turned suicidal in the end: she gave everyone else all their hopes and dreams back and had to shoulder all that negative energy herself, but she's still the girl who relived an entire month, for hundreds of loops, for one single friend and wouldn't hesitate to shoulder such a burden for Madoka's sake.
The Stinger shows Kyubey in Homura's new world, looking battered, bruised, and with its eyes glazed as if it has been, for the lack of a better term, Mind Raped. Remember his words from the series? Amongst his people, emotions are considered a mental illness... and it was just exposed to a love powerful enough (and desperate enough) to usurp God and recreate the universe. That must be the Incubator equivalent of a human getting a good look at the face of Azathoth.
Madoka promised to reunite with Homura again at the end of the series. Homura's head was "planted" with that promise, but Kyubey's interference made her break it and thus Spider Lilies bloomed because the innocent and trusting part of Homura, the Homura that became friend with Madoka would never meet her again.
On the background music, you can still hear parts (albeit slightly modified to fit the feeling of the scene) of the "Mada dame yo" song. Why? We can later see Homura lying on that weird Kyubey table as if she was sleeping. Not only that but the song says the "dream isn't over yet", and that "I wonder what color the morning will be". Of course! The movie isn't over yet and there's still much to see, and in the end, no one really knew what'd happen in the ending.
Adding on to this, "I wonder what color the morning will be" can, aside from commenting on the general surprise of the ending, be a direct reference to a new color, previously unknown to Incubators and magical girls, appearing inside her Soul Gem.
Just before she turns into a demon, Homura puts her Soul Gem in her mouth, bites down on it, and breaks it...like a nutcracker. What is Homulilly's title again?
During Homura and Madoka's conversation in the flower field, the daisies transform into dandelions. Considering that you could blow on a dandelion to make a wish...
Homura's familiars have splendid names like "Arrogance," "Sadsack," "Liar," "Coldheartedness," "Selfishness," "Badmouther," "Dunce," "Jealousy," "Lazybones," "Vanity," "Cowardice," "Fool," "Bias," and "Obstinance." And the last familiar? Its name is "Love," and it has yet to arrive. One can naturally conclude why Homura would want to surround herself with representations of her perceived negative qualities but not one of love.
On the other hand, the eventual arrival of "Love" may actually point towards an optimistic ending in the franchise, and that hope still exists for Homura, preserving the original theme of the series.
Alternatively Love is Homura herself. This seems to be supported by the clothes "Love" wears is identical (except for being bald) to the one Homura wears prior Homulilly's resurrection. So either "Love" is marking redemption, or "Love" already died and the so-called arrival will never arrive.
The guidebook explicitly called Love "A Devil". It's probably safe to assume that Homura's Love herself.
Homura's barrier has been extended to cover the entire universe. Considering what its inside is like, that's not a good news for anyone who lives in the universe... which is everyone. What if Homura's Nightmares begin to plague the entire cosmos? What if the Nightmares have become exacerbated due to Homura's extreme guilt? What if the Nightmare grow proportionally to Homura's guilt, which will eventually become too monumental for anyone to deal with, magical girls or no?
Actually, the new Homuniverse might be a good solution to the heat death problem. Both the old system with witches and Madoka's weren't very efficient. In both systems, the average magical girls on normal people ratio was about 2 on several thousands. The average lifespan of a magical girls could be anything between 1 month and 5 or 6 years after making the contract. In the old system, although the energy was harvested in both stages of witch and magical girl, most energy was harvested in the transformation between the 2 stages in which entropy was at its maximum. In Madoka's system, energy was only harvested in the magical girl stage, making it even less efficient. However, in Homura system, nightmares can come from every single person in the population of 7 billion and counting. With a little bit of despair from everyone, the collective energy would be HUGE, even with the generous way nightmares cleanse the Soul Gems. In addition to that, the energy from the magical girls and possible witches who would most definitely exist, seeing there isn't any Godoka there to cleanse the girls' Soul Gems, wouldn't hurt either. To put it bluntly, the old system was akin to the way a farmer from the Middle Age would raise cattle, the Madoka system was the more humane way that animal rights activists prefer at the cost of efficiency, the new Homura system was the way an industrialist would raise cattle: more humane than the old system but still crueler than Madoka's system, but above all, it treasures efficiency at the obvious cost of " environmental pollution" (i.e: the possible destruction of civilization). As Sir Terry Pratchett had put it: "... you had to think differently these days. Not big, but wide. With five billion people in the world you couldn't pick the buggers off one by one any more; you had to spread your effort." And if the destruction the nightmares cause goes a bit out of hand, well, that's neither Homura nor Kyubey's problem to worry about. Homura could always wave it away if Madoka's in danger, seeing as she IS the absolute dictator of the new universe.
All this is assuming the new universe isn't simply immune to the laws of physics to begin with, because magic actively protects it from all possible harm. It also allows ordinary sentient creatures and those created magically to coexist freely, which is, at least in theory, a good thing given that familiars have been demonstrating numerous sympathetic qualities in the movie. The only problem is that Homura is this world's absolute master and thus it may change in accordance with her mental state, without her explicit volition. Considering said state's fragility, the prospect might be troubling.
Take a look at the scene where Sayaka and Homura are talking in Homura's new world. Homura is acting every bit like a villain, but pay attention to what the familiars are doing. Not only do they throw tomatoes at her, but before that there's a scene where the familiars are jumping off a ledge with empty shoes on it. In Japan this is a metaphor for suicide. It's suggests that Homura is just putting on another persona, and that she's really in her own Self-Inflicted Hell.
It's also assuming that this world even has nightmares or wraiths or whatever. Given what happened to Kyubey, they might not exist at all.
And just in case that wasn't obvious enough, in The Stinger she willingly falls off a cliff.
This is also the only time where she seems truly happy. Make of that what you will.
The Clara Dolls are Homulilly's familiars and their role is playing mourners for the witch's execution. Homura is an orphan, has no other friends aside the Magical Girls and she's convinced that they will be more focused in killing her than crying for her death. She's believes that she will be Dying Alone and nobody will mourn or lament her death, so she created the Clara Dolls to give to herself the illusion of someone sad for her.
What's worse is, they won't even do that. The tears they shed are fake, as evidenced by their permanent Slasher Smile expression, and in Akuma Homura's new world their job is now to mock their mistress forever. Really, there's something very wrong with this girl.
Nagisa running around and frolicking in Homura's new world is adorable, until it hits you: it's not unreasonable to assume that considering her nature she, like Sayaka, remembers what had just transpired. But unlike Sayaka, Nagisa is over the moon. Does that mean she's okay with what Homura did...?
It's more likely that Homura already altered Nagisa's memory, as she did to Sayaka; unlike Sayaka, Homura has no real connection with Nagisa, so she'd have no reason to converse with her the way she did with Sayaka before wiping her memories.
Still, she seemed WAY too happy considering the circumstances. This wasn't her just skipping all carefree down the road on her way to school, she was out-and-out cavorting: running full speed with her arms outstretched, spinning around, dancing and laughing her head off. And then she becomes pretty much 'normal' again when she meets up with who I assume are her classmates. She was also in the 'wine world' alone with Sayaka and Homura: she could probably see it.
If the Law of Cycles is now broken thanks to Homura, what happens to the magical girls who were taken to Magical Girl Valhalla? They're essentially trapped there now, since only Madoka has the power to send agents back to Earth. Consequently, no Magical Girl will be able to go there now as well, and as Homura explicitly states, those who have returned from that place, like Sayaka and Nagisa, can never go back. It is also implied that Homura essentially created a universe-wide Lotus-Eater Machine, since she's able to alter the memories of everybody including Sayaka, Nagisa, and especially, Madoka.
There's new information on the Puella Magi wiki about Homura's seemingly decorative earring: it's the place where Madoka's powers are sealed, and the thing actually acts as a communication trinket between Homura and her familiars, but what makes it scary it's that it's partially sentient. But it doesn't end there. That tiny jewel dingling from its tail? It's Madoka's Soul Gem and its eye is Homura's.
The whole final battle is, unknown to everyone but Homura and Kyubey, a last-ditch effort to keep Kyubey from learning more about and subsequently enslaving Madoka via Heroic Sacrifice. Other than losing a few expendable bodies when containment fails, it's an unqualified victory for the Incubators until Homura makes her final play. Her actions may have subverted Madoka's sacrifice, but not doing it would have led to the benefits being completely undone.