The Zero Suit can have all the justification in the world in-game. That doesn't change its design and clear push towards sexualizing her. In Metroid Prime, Samus looses all of the powerups she has at the beginning of the game, including the Varia Suit. But she isn't reduced to the Zero Suit...
The initial reveal that Samus was a woman was a pretty significant moment for the industry, but one that was pretty poorly handled. The idea of having a female action hero in the vein of Ripley as the player character is a great one. Treating it as a surprise reveal at the end, and using her...