If I were a Lead designer? Oh, the stuff I'd do...
If I were to be a lead on the next Metroid I'd keep Sakamoto (
), Team Ninja and add Tetsuya Takahashi from Monolith Soft. Yeah. 
I'd make quite an open Metroid game with improved Other M gameplay. I'd add nunchuck support and there would be more scannable objects like in Prime.
On the Metroid timeline it would place itself somewhere after Fusion. The basic scenario would have Samus crashland on some strange planet for some reason. The locations would be huge, varied and full of mystery.
Storywise it would be quite crazy. Through some failed experiment a long time ago the planet has become one entity. The planet would be similar to an Overmind and all the planets creatures would be it's minions. Samus doesn't know this of course, and throughput the adventure she would hear the "voices of the Earth"
. Using an evolved form of the Metroid whose purpose is more controlling it's victim than killing it, the planet wants to spread to other parts of the universe. To make this happen it needs Samus, and by using different voices or inhabitants of the planet it tricks Samus into believing there are two different "factions" fighting each other, and she starts helping the "good" one.
Later Samus uncovers the truth through reading logs and when this happens the whole planet will try and make her one of it's minions.
I'd like the game to be as non-linear as possible; the world would be similar to XenoBlade with it's openess.
Like Prime 3 Samus wouldn't lose her gear in the beginning so there would be lots of new upgrades. I'm thinking about gaining something similar to psychic powers in addition to "normal" upgrades. She could take control of lesser creatures, use plants or something. These powers would only work on this planet so she would lose them at the end of the game.