The Darker and Edgier nature of Wonderland was just for the ever-present Rule of Cool as opposed to the original. Then you realize that Wonderland represents her mindset! Wonderland was whimsical in the first Alice because she was a little kid, and now she's an adult with darker thoughts!
Why everyone looks tired? A common symptom for depression is fatigue. Maybe Alice is still depressed from the loss of her father and being pressured into marriage. Also, if you'd spent years living under the tyranny of the Queen of Hearts, you'd probably look a little weary, too.
When Bayard the dog first appeared on the screen, I was a little baffled. I warmed up to him quickly (who couldn't, with those puppies?), but I didn't see the point in adding the dog to the tale, other than as another ally for Alice. It was a few days later when I remembered something — in the first book, Alice meets a puppy! Granted, he didn't speak to her then, but who's to say that wasn't a young Bayard?
When Alice first see the Hatter again the March Hare yells about how his pocket watch is ticking again. At first it seems like just another funny outburst until you watch after seeing the second movie with how Time cursed them to have the same tea party until Alice returned. The watch started again because TIME started again.
Keen-eyed viewers would probably notice the Knave's eye patch constantly changing color. At first, you think it's a continuity mistake, but then it hits you: it's only red in the scenes with the Red Queen and black in every other scene. The eye patch is a visual representation of his actual feelings: when it's red, he's faking love and adoration for the Red Queen but as soon as she leaves, it changes to black to show that, deep down, he's just as cold and cruel ("black-hearted") as any other villain.
Another idea is that he keeps two eyepatches on him, one red and one black. He wears the red one when he's about to see the Queen of Hearts but changes to a black one as soon as he's out of her sight. This would also fit in with how members of her court wear prosthetic disguises to make a part of their body look unnaturally large.
Mad Hatter's fits of rage. To be honest, they didn't 'bother' me, but they just came behind the tree from one point, for seemingly without any provocation. Then I started to think: He's supposed to have a mercury poisoning, right? I looked up the symptoms and the mystery was solved. The poisoning hyperstimulates the heart and causes insomnia, but slows the adrenaline glands. Adding the state of Wonderland and his own personal demons it's clear, that he is constantly under stress without the way of releasing it, making the Hatter a ticking time bomb. The pressure builds and builds, until he flies to rage from even the slightest thing, even if someone even mentions something unpleasant.
Underland/Wonderland seemed like much more of a safer place when Alice was a little girl. Well, there's something that should be considered: in the original novel, whenever the Queen of Hearts would send someone to their execution, the King of Hearts would pardon them before it could be carried out. With the king dead, well, you know the rest...
Recently had this breakthrough: it had started bugging me a little that the residents of Underland were so set on following a prophesied path. I mean, the whole point of the place is that everyone is mad, so why should they care about prophecy so much? Why not make their own random paths? Then today, I remembered something from "Through the Looking Glass" — Wonderlanders, or at least Looking-Glass Landers, can remember things backwards and forwards. To them, they've already remembered what's going to happen! (Hell, when you think about it, isn't a prophecy sort of like a memory of the future anyway?)
How about this one: at the end of the new film, Alice goes to open trade with China. Historically, this was done by the British Army going to war with China in order to sell Opium. Here's the brilliance: the majority of Alice in Wonderland was written by Carroll when he was regularly taking Opium. Alice is retroactively ensuring her own existence!
Well, yes and no, possibly, seeing as the fictional Alice was based on the real Alice Pleasance Liddell, a friend of Carroll's.
This is a very minor detail, but in that scene where the Red Queen orders the frog executed and his children brought to her, she says, "I love tadpoles on toast, almost as much as I love caviar." The first two times I saw this movie, I thought the horrible thing was that she was treating talking animal kids like food. The third time, I realized that she's talking about eating caviar—to a fish! That's just wrong!
It's been mentioned that Alice is wearing a dress that's more suitable for young girls than a nineteen-year-old. But, with everyone else wearing age-appropriate attire and people constantly telling Alice that she should be married by now, one must wonder if Alice's mother decided to make Alice look younger, and therefore more proper.
Her outfit also pays homage to Alice's look from the animated film. Her black and white boots even look a bit like the Mary Janes that Alice wore as a little girl.
At the beginning, the White Rabbit says he had to follow a lot of Alices - of course he would! Alice was a very common name in 19th-century England.
It's rather fitting that a Feathered Fiend be the one to snatch up the Tweedles for the Red Queen; after all it was the "monstrous crow" that ended the poem the two originated in.
On that note, the remark about enjoying tadpoles on toast. Since animals in Underland are as sapient as humans, this means that the Queen of Hearts literally Eats Babies.
Since Alice opened up trade in China, does that mean Alice caused, or helped cause the Opium Wars? Either she brought something/someone she shouldn't have or made a big mistake to do that. That could also mean she has blood on her hands.