In an Iwata Asks interview about Metroid: Other M, Team Ninja head and Other M director Yosuke Hayashi classifies the game as "a NES game with the latest technology," an ideal that went on to inform much of the design. "Yes, we thought that if we could make a game that could be controlled with just one Wii Remote controller," Hayashi told Nintendo president Satoru Iwata, "we'd enable players who were put off by complex controls to enjoy 3D action games as well."

The automatic movement of perspective enabled the game to have 3D environments while maintaining simple controls, and clever Wiimote movements like pointing at the screen to explore in 3D allowed the team to avoid "resorting to the Nunchuk," as producer Yoshio Sakamoto called it.

At the same time, Sakamoto wanted the story and action to blend seamlessly, so the team worked with video production company D-Rockets. Director Ryuzi Kitaura described creating detailed storyboards to impress Sakamoto: "I think I drew more than 300 storyboards in total. The image count was over 2,000. By this stage, I was also accounting for camera work and action, so they became really elaborate production storyboards. I think I took over six months to finish them."