The first game within the Metroid Prime series to use the 'stacking' system in weapon upgrades. This means that weapon upgrades add new abilities to existing weapons (as in Super Metroid (1994) and Metroid: Fusion (2002)), instead of adding new selectable weapons, like in Metroid Prime (2002) and Metroid Prime 2: Echoes (2004). The main reason for this is that the button lay-out of the Wii controller did not allow for an easy switch between weapons while playing the game.
Samus seems to have different ships at her disposal for different needs: while the ship she used in Metroid Prime (2002) and Metroid Prime 2: Echoes (2004) shows great resemblance to her ship in Super Metroid (1994), the ship in this game looks very much like the one used in Metroid: Fusion (2002) (albeit with different colors).
The first game in the Metroid Prime series where an in-game feature can be activated that reveals the location of all (remaining) Suit Expansions. The Chozo Observatory on Elysia can be used to enable this feature. In the previous games, Suit Expansions only made a distinctive sound that would indicate if one was near, so collecting all of them for a 100% score often required a lot of searching, or help from outside.
The music heard on the Pirate Homeworld after retrieving the Hazard Shield is the same as the Space Pirate theme heard while exploring Crateria in Super Metroid (1994).
Like in the previous two Metroid Prime games, Samus' face is being reflected in her visor. This is best seen when using the Scan Visor in a dark area. Her face appears normal at first, but as Samus' body becomes more corrupted by Phazon over the course of the game, her face appears progressively more disfigured.