According to concept art, Alice's dress was to feature the symbols seen in the first game, the symbol of Venus and a sextile, as opposed to the symbol of Eris and symbol of Jupiter seen in the final game.
In Chapter 4, inside the Queen's castle, the floating platforms look like the Weighted Companion Cube from the Portal series.
In a prerelease trailer for the game, Alice can be seen swimming in the Deluded Depths. This was cut from the final version and Alice simply runs across the ground as she does in the other areas of Wonderland.
Spicy Horse executive producer R.J. Berg wanted Alice to use the umbrella to glide around like Mary Poppins but it was cut due to "technical complexities". The umbrella was supposed to be the main weapon used in both fighting and exploration.
In the Doll Maker's Domain you can find a reference to the classic nursery rhyme "Three Blind Mice". There are three mice in a jar wearing sunglasses and one holding a cane.