Metroid series father Yoshio Sakamoto recently admitted that a similar game to Other M wouldn't be possible without Team Ninja.
In an interview with CVG, Sakamoto explains that "if we are going to make something similar to Metroid Other M in the future I cannot think that it would be possible for Nintendo to make it without collaborating with Team Ninja." He also praised the studio, stating that he is "very grateful" for the Nintendo/Team Ninja collaboration in making Metroid: Other M.
If Nintendo are going down a similar route and story design for the next Metroid game, then Team Ninja would be the likely candidate to take the role. Sakamoto feels that if a new game will take on a different direction, then another partner might be possible.
In another recent interview, he noted that new Metroid plot would follow Metroid Fusion in the series timeline.