Course Elements are unlocked through the Super Mario Challenge, rather than having to wait for a set amount of time. In addition, there are different course elements unlocked from the start.
Checkpoint Flags, Skewers, and Keys are now standalone course elements.
Different players can collaborate on courses together via Local Play.
Upon starting the game for the first time, the player no longer needs to play though an unfinished course and a guided tutorial before being able to access the Main Menu. Instead, the player is greeted with an introductory speech from Yamamura and Mary O.
When placing an object down in the course editor, instead of a distorted voice saying the name of the object, there is simply a small sound that sounds like two sticks tapping each other.
The course elements interface now has seven columns with nine items each, as opposed to the Wii U version, which has five columns with twelve items each. Also, there is no longer a crown column, and all items completely fill each column.
There is a glitch where if the Super Mario Maker for 3DS cartridge is inserted into different 3DS, all progress is reset, even is the cartridge was put into the owner's 3DS. If the Disk is put onto a different Wii U, there will be no progress. Once the Disk is in the owner's Wii U Console, his/her progress will still be there.