Cora: did she really considered the Red Queen as a replacement for her daughter like she claims or did she only use her as a pawn to get rid of her rival king, then rule all of Wonderland? Given some revelations in the fourth season of the main show did she choose Anastasia because Regina no longer can have children?
The Jabberwocky: Was her change of side genuine or did she intend to backstab Alice after Jafar's defeat?
Complete Monster: As the Big Bad, Jafar is as bad as it gets. A true Bastard Bastard and Evil Sorcerer extraordinaire, his plan is to enslave three genies and use their combined magical powers to wish for the rules of magic to be changed so that he may become the all-powerful ruler of Wonderland. Cruel, utterly ruthless, devoid of empathy, and detached from humanity, not an episode goes by in which he does not threaten, manipulate, torture, murder, or all at once in order to get what he wants. Jafar's most noteworthy atrocities were changing the woman who loved him and taught him sorcery into his serpent staff, threatening to murder Alice's father in order to make her surrender her two remaining magic wishes, and not only murdering a young woman in cold blood just to get a reaction out of her lover, but later reviving her and making her fall in love with him right in front of said lover, who is powerless to stop it. Worst of all is that we're led to believe that he ultimately just wants love from his abusive father and wishes to change the rules of magic in order to force him to give him affection, but it's revealed that he really wanted to make his father love him so that the peace of mind and vengeance he'd get out of murdering him afterwards would be sweeter. In the end, all Jafar truly wanted was power to do whatever he pleased with.
Of course, comparisons between the Red Queen and Regina are inevitable...
Jafar's getting it too, regarding his similarity to Rumple.
Ironically, this is switched around in terms of motivation. The Red Queen made a mistake and chose power over someone she loved and now does bad things while seeking a way to make up for it... just like Rumple (she also has a similar verbal tic, "darling" instead of "dearie"). Jafar has an abusive parent whose love he desires and who he grew up to be just like in spite of himself, doing maliciously heinous things at least once per episode... just like Regina. Unlike Regina, however, Jafar's problems aren't rooted in his parent lacking a heart; just plain stubbornness on the part of said parent.
A lot of people have been comparing the Alice/Cyrus relationship to Snow White/Prince Charming's.
And now we have Jabberwocky who seems set to be this series' Cora as an extremely powerful female with a knack for getting into people's heads.
Alice and the Red Queen in "Heart of Stone", rather disturbingly. Not really on Alice's end, which is just a case of Teeth-Clenched Teamwork, but the Red Queen's demeanor and habit of calling everyone "darling" makes it hard not to see it on her end in this situation.
Also, while the "Foe" part doesn't last long, several fans sensed some chemistry between Cyrus and the Red Queen during their scenes together in "Who's Alice" and "Home".
The Cheshire Cat's remark to Alice is that he would not eat a friend "not without pepper"; in the original book the Cheshire Cat is the pet of the Duchess whose Cook is a pepper addict, so his comment refers to his former owner.
It seems bizarre that so many of the citizens of the supposedly Arabian Agrabah, Jafar included, are portrayed by actors of apparent Indian descent. Except there are theories that 1001 Nights originated with Indian stories.
Alice has good reasons to be upset at her father, from blaming her in her childhood for the death of her mother to neglecting her in favor of his new wife, then never going to visit her the year she was in the institution. However according to both Alice and the narrative, Edwin's biggest fault was... not believing Alice when she told him about her adventures in Wonderland, which is nonsensical. If you're a rational man unaware of the existence of magic, then your daughter tells you that she experienced fairy tales without any evidence, you'd be forgiven to think she's mad no matter how much you love her. Whether that does justify succumbing to the demands of an overbearing wife to send away your own daughter rather than find a compromise allowing them to stay together under one roof, however, is another story.
For that matter, the narrative spends a great deal of time showing Jafar's cruelty in how he imprisons and mistreats a certain old man in his dungeons, who is eventually revealed to be his father the Sultan. However, just prior to this it is also revealed that the Sultan rejected and abused his son for being a bastard, and even tried to murder him in order to get rid of what was to him a politically embarrassing and morally repugnant mistake, thus making the present scenes of Jafar's actions in the dungeon seem a lot more understandable, if not justified. It is implied that the old man has come to realize the error of his ways, and regret his past actions, thus swinging the sympathy back to him and making Jafar's actions wrong... until he reveals his only regret is not having succeeded in killing Jafar and preventing his evil. The very evil he actually created by his initial treatment of him. Eventually he claims he does regret what he did, yet he continues to act antagonistic toward Jafar in a misguided attempt to change him by again offering his love on a condition, this time that he stops doing evil. By the end of the show, the viewer is still expected to feel sorry for the old man after Jafar forces him to love him, then kills him; his fate is terrible, and it doesn't justify anything else Jafar did to get to that point, but it does make him something of an asshole who deserved what happened to him and creates some Moral Dissonance, since he never seemed to fully learn his lesson.
The Red Queen for all the abuse and intimidation Jafar heaps on her.
It gets worse when we find out she's the Knave's old girlfriend Anastasia and see what a sweet, innocent person she was until her emotionally abusive mother's influence finally overcame her and she became Queen at the cost of her love, and the regret of that choice and desire to undo it is what drives her now.
Will Scarlet, who had his heart broken by the girl he loved and then had his heart flat-out lost at some point, after which he became the evil Knave of Hearts who committed many crimes... and even after getting his heart back, he hasn't put it back in his body because the feelings it gives him are too painful.
The Grendel from episode 3, a ruthless cannibal who could never let go of the memory of his beloved who left him. More than a few fans were devastated by Jafar killing him.
Young Jafar spends the few minutes of his screentime in "The Serpent" as one, being an abused street rat disowned by his father the Sultan for being his bastard son. It's WAY downhill from there, though.
We see even MORE of young Jafar being one in "Bad Blood", and even present-day Jafar earns a little pity when learning what his motivation is.
Subverted in the finale, where it's revealed that his motivations regarding his father were revenge rather than love, and his long-term motivation was absolute power to do whatever he wanted, removing any possible sympathy one could have left for him.
Love It or Hate It: This series is much more divisive than its parent show for various reasons.
Jafar seems to be one of those "multiple choice" villains when it comes to this trope, as he murders, tortures, manipulates, and generally does any sort of cold-blooded act at least Once per Episode. Common picks are killing the Grendel, betraying and murdering his teacher/lover Amara, nearly killing the Knave before turning him to stone, using his magic to physically torture Alice, kidnapping Alice's father and using him against her, and releasing the most evil creature in Wonderland to assist him, despite all warnings of what disaster this might bring.
He ends up topping himself in episode 11 when he murders Anastasia right in front of a newly re-heartened Will just to test if that heart is working.
He manages to even top that in the finale, by using his new power to bring back Anastasia and make her love him. He claims it was for a purpose, but it's clear that he actually did it just to be a dick.
Jafar is a generally terrifying villain, but his hammy roars of "RRRRRRABBITT!!!" to the fleeing White Rabbit in "Heart of Stone" will probably elicit more laughter than fear.
He does it again in the finale, with the line "with nothing but a sword and a RRRABBIT!" That last one is the only word he raises his voice at.
The last shot of the twelfth episode: Jafar looks silly open mouthed and with glowing white eyes. It looks like Jafar is entering the Avatar State. Come to think of it, a Jafar-looking Avatar was spotted in The Legend of Korra.
Jafar was also difficult to take seriously in the first three episodes of the show due to his ridiculously curly long hair, which brought much amusement and mocking from many viewers. Thankfully, the producers quickly amended this, so in the fourth episode and onward his hair is shorter, more natural and stylish.
Narm Charm: The bad CGI, for some. Somehow, it works in a bizarre world such as Wonderland.
Become less so as the show went on, and now the feeling has all but vanished since it's been revealed that Cora is who made her the new resident Evil Queen to begin with.
Rescued from the Scrappy Heap: When the show premiered, the Red Queen was not very popular at all. The ending of the second episode, however, where she successfully pulls one over on Jafar and stands up to him, changed many a viewer's mind. The subsequent Hidden Depths shown in following episodes just pulled her out of the heap even further.
She Really Can Act: Emma Rigby was considered by many to be the weak link amongst the cast but "The Serpent" and "Heart of Stone" which show her conflicted feelings for Will have earned her praise and made many realize that the former stiff acting from her was deliberate, as that's just what the character's demeanor is in-universe: a stiff act. And if there were any doubts, "Home" obliterated them with a total Tearjerker of a performance when the stiff act crumbles and gives way to scared, sad, lovelorn Anastasia. And she just kept on knocking it out of the park from there.
Also the White Rabbit's family, which is such a pity given how decently-rendered the White Rabbit is.
Stylistic Suck: One of the possible explanations for the poor CGI backgrounds for Wonderland, compared to the Enchanted Forest and the rather well done creatures, that it's to emphasize the magical and otherworldly nature of Wonderland.
Oddly, the Cheshire Cat, one of the most iconic character of "Alice In Wonderland", only appears in one scene in the pilot.
Elizabeth "The Lizard" introduced in "The Serpent", an Action Girl who shares a past with Will and is a potential recruit in Alice's gang. She vanishes after her introduction episode. She comes back a few episodes later where she accidentally kills herself by making a poorly thought wish.
Too Good to Last: The show was always designed to feature a one-season story, and would pick up additional seasons with new stories if it was a success. Sadly however, due to a bad time slot, the ratings were dismal, meaning no new episodes are to be ordered. Though Will then joined the parent show as a recurring character, indicating at least some of the ideas for where the show might go next have been absorbed there.
The Red Queen being one of Cinderella's stepsisters was guessed long before it was revealed.
The Sultan being the old prisoner, more so. Many fans guessed it after "The Serpent" aired, but throughout "Bad Blood" it was painfully obvious before The Reveal.
Visual Effects of Awesome: Despite all the bad CGI for the backgrounds in Wonderland, the CGI creatures are actually genuinely impressive. The White Rabbit and the Cheshire Cat stand out especially.
What an Idiot: Some fans believe Alice's wish to save Will (if Will dies, she dies) was risky and poorly thought out when she could have wished herself, Will and Lizard to safety or wished Jafar and The Red Queen away from her. It does bite her in the ass in "Home".
Not that Alice is the only one to make poorly thought out wishes after Lizard made the mistake of using the phrase "I wish" around a genie when the only way to grant said wish involved killing her.
The White Rabbit. He may be a coward, but his heart is in the right place and with all the shit he has to face, it's not hard to see why he's so cowardly.
Alice. She felt unloved by her father, saw her love falling to his apparent death, then got back home to find her father married to a woman who doesn't seem to like her, was mistaken for a mad girl by the father she only wanted love from, and then spent a whole year in Asylum crying every night. And that's not counting all the shit she deals with in the present-day story...
Anastasia/the Red Queen, formerly a Jerkass Woobie, graduates to full-fledged Woobie status in "Dirty Little Secrets", and it only got worse in "Heart of the Matter", which culminates in her death. She gets better (twice) in the Grand Finale, fortunately.