Metroid is amazing. But it's not something that attracts a big audience, let alone on a Nintendo platform.
Metroid Prime 4 could do well if they ever finish it. It just doesn't have the same 'nostalgia' as Mario and Zelda and it isn't easy to reinvent like Fire Emblem.
To this day I think Nintendo should've picked up the cancelled Prey 2 and retooled it into a Metroid game. It would've probably given the franchise the mainstream boost it needed.
The Metroid universe is limited by design and Nintendo's usual tricks to spice things up just don't work. The Half Life / Unreal guys that made the Prime trilogy were the perfect fit for the series.