

Water surfaces no longer ripple in reaction to weapon fire or character movement (although the water will still splash), and the Arm Cannon is no longer affected by the type of beam it is charging. Certain special effects from the GameCube version of Prime were removed due to technical problems.A Bonus Credits system similar to the system included Metroid Prime 3 allows the player to use Credits to purchase extras such as a Screen-Shot Tool, Fusion Suit, music, or image galleries.When starting from a previous save, Logbook scans will be retained.The Normal Mode in this version is actually a new, much easier mode, with Veteran being comparable to the GameCube version's Normal. There are three difficulty settings: Normal, Veteran and Hard.The main menu has been changed for the Wii, and features the same text boxes used in Corruption.New clips are present in the attract mode.An intro video on the Disk Channel of the Wii's main menu has been added, featuring the game logo and menu theme.Bloom lighting and widescreen support are featured. Textures and shadows are sharper and clearer.The Scan Visor Sight Window is circular instead of rectangular, with an additional central reticule added.Unlike Corruption, if Samus aims at the center of the screen and keeps the Wii Remote still, she will put her hand on the Arm Cannon.When the Wii Remote aims at the edge of the screen, the HUD withdraws and shows a white circuitry pattern like the one in Corruption.The Visor HUD does not display all the visors and beams collected, only the one in current use.The motion-controlled Spring Ball function is included, which is activated when Morph Ball Bombs are acquired, as well as all of the customizable control options.

Most of the controls remain the same as those in Corruption, except that the + button is used to change Beams.

The game's commercial features Samus being controlled in third person.
