The first game within the Metroid Prime trilogy to use the 'stacking' system in weapon upgrades. This means that weapon upgrades add to the power of existing weapons (as in Super Metroid (1994) and Metroid 4 (2002)), instead of adding more 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 4 (2002) (albeit with different colors).
Samus uses her morph ball to avoid boss character twice in the game's cut scenes. This first is to avoid the shots fired by Gandrayda mimicking a Federation Trooper, and the second time is when she is attacked By Omega Ridley.