American McGee's Alice/WMG

Destroying the Red Queen destroyed Wonderland
That's what the Queen meant when she said 'If you destroy me, you destroy yourself.' As the tentacles everywhere imply, she and that world were so linked together that her destruction meant the world's destruction, and completely forgetting that crazy place is the only way Alice could become fully sane. That end cinema where everything was restored was actually the last thing the Wonderland residents saw before being annihilated.
 * Jossed in Alice: Madness Returns in which Alice and madness return to Wonderland.

The White Rabbit is actually on the Red Queen's side
He was the Queen's herald in the original books, and is continuing to serve her by trying to get Alice to give up her quest. Him constantly eluding Alice was meant to confuse and disorient her and his death was staged so Alice would feel guilty and depressed, which would impede her progress and give the Jabberwock more power.

The Mock Turtle is actually on the Red Queen's side
The business with his shell was really a ruse so Alice would kill the Duchess, who the Queen wants dead, and so Alice would have a bit more blood on her hands. The real reason the Turtle gave Alice something to help her breathe underwater was so that the Queen's minions could have the pleasure of killing Alice rather than have her just drown, which is much less delicious. If the Turtle was still a good guy, why doesn't the Gryphon, his best friend, ask if he's alright or something?
 * Jossed i'd say, in the sequel (where the Gryphon is dead) he built a ship to commemorate him. Oh, and he didn't ask anything because he didn't appear after the Vale of Tears.

The teasers and promotional material for Madness Returns hint at Alice in Wonderland characters who will appear in the game.

 * In the first teaser, you can see a stuffed dodo in the room, hinting at the Dodo and possibly the rest of the caucus race.
 * In the second teaser, there is a shop called 'Walrus Carpenters' and, in the background for the official site, there is a card featuring a figure with a pencil on his ear, and nails in his head, hinting at carpentry. Therefore, the characters of the Tweedles' poem will likely appear in the game.
 * The second teaser also shows a statue of a lion, underneath deer heads, a possible foreshadowing of the Lion and the Unicorn.
 * As Alice approaches the dolls in the second teaser, a butcher shop with a sheep head above it can be seen in the background. Wasn't there a sheep with a shop in Through the Looking Glass?
 * Partially confirmed, as the Dodos, Walrus and the Carpenter appear. The members of the race have a cameo as frozen corpses in Tundraful.

Madness Returns will be to American McGee's Alice what Through the Looking Glass is to Alice in Wonderland
Promotional material shows that Madness Returns will have more plot than American McGee's Alice, like Through the Looking Glass had more plot than Alice in Wonderland. And like Alice in Wonderland was about Alice trying to sort out her size and find that beautiful garden, American McGee's Alice was about Alice trying to sort out her mind and find that beautiful sanity. So maybe Madness Returns will have Alice become Queen again?

There will be a third game
It's a gut feeling.

The game shares a universe with Psychonauts
Self explanatory to anyone familiar with both games.