Speaking of upgrades, they should bring the speed boost back. Just so it's not stressful on the eyes, they should use the trick most other ones do. Simply make the world around you go in extreme slow mo. That gives the illusion of speed.
Who knows they might make a Metroid Prime 4: Resurrection .
It could be a 3D remake of Metroid II: Return Of Samus but longer and with more features or it could take place after Metroid Fusion. Also maybe it could add the Mother Brain from the orignal Metroid trigoly and make it the final boss in Metroid Prime 4: Resurrection. It could play like the final boss in Metroid Prime but maybe a little harder and also bring back the old villains like Kraid. Metroid Prime 4: Resurrection could make a comeback to the 2D series and bring it all in 3D. It will also add some new characters and villains. It could come out in 2010 depends on Retro Studios descision.