The great thing about Nintendo franchises is its heavy focus on gameplay more than any other. Other M was a great game but it being story-driven coupled with strictly limited controls gave it niche qualities even more so than the Metroid franchise already is; Controls are an integral part of gameplay.
Legend of Zelda's story is a given, while Metroid's story is readily available only if sought out (Scanning).
I enjoyed Other M for its different appeal. I, however, felt a little resentful towards Nintendo in their consideration of the Prime series as not being part of the canon. I may just be reading too much into it, though.
Either way, the best we could hope for, if the series have what it takes, is a split in the series similar to how Mario is now: 2D and 3D.
