The best new gameplay mechanics start simple and stay simple. Where they grow is in the limits placed on them, not in the complexity of how the overall system works.
Take Portal, for example: they could easily have made it so that portals can be formed anywhere, so there were far more colors of portals, so that you could use portals to go back to any point where one had been placed no matter how long ago it had been put there, and so many other things. But they didn't. They set very clear limitations (no portals on metal, surface has to be big enough, only two portals, new portals erase old portals of the same color). And those limitations refined the system to the point that it was a solid, workable system with understandable mechanics that could be picked up quickly and applied in a dozen different ways with less than an hour of practice.
If they can find a way to have a similar impact with some existing Metroid sub-system, that'd be great. But I suspect a new sub-system entirely may be a better move...
Sky Render - Sanity is for the weak.
