I think that it is too late to think of improvements for the next Metroid on GameCube.
I like your ideas Gamefreak, I've been thinking about a lot of them myself, but I've been trying to visualize what a Metroid could be free of the restraints of the Cube. As powerful as the Cube is, the Revolution/N5 will have real lighting in the games that will make what Splinter Cell and Doom 3 have done this generation with real time lighting look less than standard. With real time lighting as standard tool for the next system, I can't wait to see what Retro can do as far as atmosphere and visors. More importantly for control, the controller will have improvements over the present Cube controller.
Something as simple as mouse wheels for scrolling through visors, and weapons could unclog the control in the next Metroid. Halo 2 gets rid of one quality that made Halo so good; it had multiple control layouts that were for the most part pretty functional. Say if you wanted to control with the right analog stick and look with the left then in the original Halo you could reasign the left trigger from being grenade to being jump so that you can jump and look and run and shoot at the same time (having the right trigger as primary fire). Unfortunately Halo 2 has melee combat (that requires targeting, they stole from Metroid too), you also have dual wielding which means you have to put your jump on A button (which means you have to use the right analog stick to look so you can still move while you jump, but you can't look, jump, shoot, and move at the same time anymore), and you can't reasign jump to the Dpad on the Xbox controller for Halo 2 so you could still move with the right analog stick. With having the independent use of each arm, which most people want to be standard, we sacrifice, at least camera control, if not more with the present controlers. Halo 2 suffers from what Metroid Prime suffered from. Slow movement even though you were in an advanced cybernetic space suit built for combat along with linear control. The deathmatch in Halo 2 has been said to be a bunch of people standing and shooting because you really can't dodge or jump fast. In Prime we were forced into using the ball because Samus wouldn't run fast (I guess I want Samus to run, jump, and straff faster than most any character, but I want the morph ball to be able to go ridiculously fast).
If Nintendo uses tilt technology gyros in there next controller along with dual analog then camera control can become a worry of the past. I suggested mouse wheels earlier to replace weapon and visor selections. One can think of designing the game and the options around a layout like this. Each trigger, with its digital click, can be used for each arm instead of the face buttons. I would suggest the analog sticks to be capable of reasignment (classic Prime controls, and other new variants). I like the idea of using the grapple beam in combat, to throw enemies and objects. The grapple beam could be on the left trigger. You could control the character movement (forward, backward, straff left and right) with one analog stick, the camera with the other analog stick, and the actual aim (or drag since you would be using the grapple beam like a whip latched onto something) by tilting the controller. I assume you would see Samus' breastplate instead of her feet when you looked down. You could jump with a face button, which could be on either side if they get rid of the useless dpad and put two sets of face buttons on the controller. You could also choose to use the A button for the grapple beam and use the left trigger for jumping. I believe that the lock on, should stay in the game to assist in aiming. Though you would have total control over camera and aiming, Samus' ability to auto aim is a nice crutch that other first person shooters don't have.
Melee attacks scare me though. I'm afraid Metroid would become like the brawler Castlevania on PS2. If the controller had two sets of face buttons with jump on both sides, then you could use x, y, and b on one side for morph ball, cloaking, and map; and use the other set of face buttons for punches, kicks, swipes, and grabbing and using an enemy body for use as a shield. Missiles and lock on could be put on digital Z buttons under the triggers for the middle fingers.
I really like the idea of using other characters in the multiplayer (coop would be better than deathmatch) other than Samus. Nothing would make people appreciate Samus' suit more than playing against it. I think the idea of having different visor technology for each character (pirates, marines, Samus, Chozoa, Aethers, Dark Samus, Omega Pirate).
I would like a storyline where the Pirates try to capture Samus for her brain to replace Mother Brain after Samus killed her, but then they capture the Dark Samus and her suit and they don't know it.