What if:
Samus was fighting this giant boss, whose attack was to suck things in (including samus). As the beast prepares the attack, Samus would have to first grapple beam herself to a hook. Then as she's literally hanging horizontal to the ground, you have to manuever your cannon in the general direction of the beast and charge and fire a super missle. Meanwhile, your view is going hay-wire as you shake with turbulence.
I think that would be a pretty cool boss.
Or What if:
Samus grapples to an object and the only way to blow it up is if you aim at your grapple beam (after aquiring the Wave Beam) and shoot a charged beam at it. The beam clings to your grapple and follows it like a trail of lit gun powder.
Or What if:
There is a boss that travels furiously fast, is enourmously huge, and is the first water boss in Metriod history (i think). Samus must grapple to it's back and she hangs on for dear life, water ski as she tries to kill the damn thing! Knowing Retro, it would be crazy!
Or What if:
Samus obtains the ability to use bombs outside of her ball state. She grabs a bomb with her left hand and with the nunchuck, chucks it where ever she likes. There are two settings for the bomb: Gravity and Anti-Gravity. Gravity acts like a normal grenade, while Anti-gravity floats upwards very slowly. While Gravity bombs blow up on impact, Anti-gravity bombs must be shot. Anti-Gravity bombs also cause a much bigger explosion.
Or What if:
One of Samus's grapple beam upgrades turns it into a laserbeam type sword. Not neccessarily to attack with since that is not Metriod at all, but more to cut through vegitation, carve through blast-proof windows, and things of that nature (another way to advance exploration basically).
Or What if:
One of Samus's grapple beam upgrades allows for more than one grapple. This would be used to pull multiple triggers (similar to how Zelda's boomerang can lock on to multiple items, and used in basically the same fashion; i.e. puzzle-solving, boss-battle, taming a gaint beast to fly or swim). OOOOOOOOH!!!! That would be amazing! Imagine using a giant manitee to explore an ocean. You can still shoot with the Wiimote. The nunchuck, however, would steer the beast (or it could steer itself, probably better). Or what if you used a giant pterodactyl to access a new area, only to be shot at by Flying Space Pirates. That sounds like a sh!tload of fun, especially if the beast reacted to the shooting and swooped and tried to dodge.
Alright, that's enough for one day. You guys get the jist of it anyways...