Super Mario... (wait for it)...
The working logo for the game was very simplistic, only reading "Super Mario" and having a Bob-omb by the side of it.
Now you see me, now you don't.
In the game's code, another playable character can be found. By making it appear on the screen select menu, it appears to be named Oh shucks, this appears to be an error. (Even tho it's cut a bit) although in the game's code it's referenced as Toad1.
In game, it looks like a glitched up Blooper, and selecting it crashes the game.
Super Mario 3D Galaxy... Maker?
One of the entries in the game's code is for Builder3DS. Activating it allows you to enter a menu where it will ask you to put a game called Super Mario 3D Galaxy Maker on a 3DS and connect it to the console.
Obviously, this game doesn't exist, but some gameplay screenshots are shown in the menu.
The concept of the game was that you could make your own levels like in Super Mario Maker, but you'd have to play them on your console in Super Mario 3D Galaxy. It was most likely a free game.
Tech-not polished Mushroom
Originally, the Technocolor Mushroom had a very ugly and unprofessional appearance. It was a mushroom with different colored mushrooms around it. It was replaced with a way better design.