E3 2014 | Nintendo has Plans for Both 2D and 3D Metroid Games

Just let Samus explorer a planet. Give it the normal organic esq style/Farscapey visual style.
Use the Xenoblade knowledge you are (probably) already using for Zelda and you got a solid base already.
Chuck in some actual bountry hunting, and some new weapon types (say, stuff like Gravity, Poison, Madness) as well as new combination effects (Beam gravity on an object everythings attracted too it, beam gravity on a enemy and the other enemys go smashing into it).

Visor wise is the only thing I think could have a major revamp. Rather then discrete spectrum pieces ("X-ray" "Inner Red" ) like before, have the whole electric magnetic spectrum viewable, and a slider bar on the touchscreen showing how that translates to the colors we can see.
Yeah, behind the scenes this will be fancy HDR color maps and physical light mapping stuff - but for the player it will just be pretty color awesomeness they can control to see different things

Oh, and finally, it turns out that Alex Rovas is Samus distant ancestor, and Samus ends up fighting Cthulu.*

*I might have got carried away with that one.

^this

Not my vision but it will do.

Sounds good.

Trippy!

Get to work retro.

Haha nice Eternal Darkness reference DarkFlame. The visor & weapons ideas aren't bad & I've always felt they should explore her bounty hunting aspect more. Make it a way to earn in game currency so you'd have to buy upgrades instead of just finding them.

Keep exploration & secret discovery of course but make it feel like she has to pay her bills as well, that gunship doesn't refuel itself you know lol.