In an Ask the Developer interview by Nintendo, Takashi Tezuka said that the need for a new side-scrolling platformer came out of necessity from him. According to Tezuka, many journalists and players felt that the Super Mario Maker franchise would have ended the need for another 2D Mario game. Tezuka, however, always felt confident that Wonder would be completely different from other side-scrolling Mario installments.

Coming up with brand new ideas was a challenge for Tezuka and his then-small team, and resulted in over 2,000 different ideas on how to make Wonder look fresh and out-of-the-box.