There was a rumored Game Boy Color port of the game called "Metroid II: Return of Samus DX" featured once in the German gaming magazine "Club Nintendo" that was claimed to make use of the Game Boy Color's vast color-palette. However, the game never released and its existence has been contested by a testimony from Nintendo of America translator Dan Owsen who was unaware of plans for the port, suggesting that the screenshot featured in the magazine may be a mock-up.

There are a few inconsistencies between the appearance of the Omega Metroids in Metroid II: Return of Samus and the one at the end of Metroid Fusion. The first is the size of it, as it was 150% Samus' size in Metroid II, but is now twice her size. This could be linked to the baby Metroid in Super Metroid, who grew larger late into the game. Another inconsistency is the fact that it's only weakness in Metroid Fusion is the Ice Beam, when the Ice Beam had no effect in Metroid II.

The signature large shoulders of Samus' Varia Suit debuted here and were born out of necessity. In the previous game, the Varia suit was shown as a pink palette swap of the normal suit.

Because of the Game Boy's limited color palette however (it could only display around 4 different shades of black and white) drastic visual changes had to be implemented to let the players tell the Varia Suit from the normal suit. The Varia Suit was thus given larger shoulders which have since become the most defining feature of Samus' armor throughout the series.

This also affected Samus' Arm Cannon's missile launcher function. In the previous game, Samus' Arm Cannon turned blue when its Missile launcher was active. However, because of the limited color palette, in Metroid II, Missile mode is shown as the tip of the Arm Cannon opening and extending outward which has also been featured in later games.

Metroid II: Return of Samus and its remake Metroid: Samus Returns are the only games in the series to not feature a timed countdown sequence. Instead, Samus leaves Phase 9 with the Baby carving out obstacles for her.