Samus is hardly an exception; put into a suit that erases secondary sexual characteristics, the question of gender was (in the first game) left until the last possible minute, as nothing more than a "gotcha." In future games, Samus's gender is still hidden behind the suit.
And the one game where they tried to actually make a character of her, Other M, portrayed her as embarrassingly weak-willed (making sure to make it about her gender as obviously as they could, no less) and verging on obsessive toward her (male) superior officer.
Metroid is a great series, but they do not win points for this.
The saddest part of Other M might be that its development was lead by the surviving co-creator of the original Metroid games, who does not appear to understand why people liked Metroid in the first place.
With all due respect, if Nintendo were to introduce Samus with the blue suit that she's wearing in the latest game, then we would have other kinds of problems, mostly to do with how female characters are designed to appeal the male audience. My personal preference is that I like her wearing the classic yellow suit. After all, if a male can wear protective gear when he fights against pirates in space, I don't see why a female shouldn't.
To be fair, the only games where the zero suit is featured except for the end game are:
* "Metroid: Zero Mission" She crashes, and thus doesn't have the power suit (for a while). Also, it was for the GameBoy, so the sex-appeal isn't as strong.
* "Super Smash Brothers" is probably the worst offender. (not a Metroid game)
* "Metroid: Other M": It apparently has minor occurrences throughout.
Everyone who plays the series today know she's a girl, though. The "reveal" gimmick of the first game is long forgotten and probably says more about this issue in the 80s than it says about it today.
In the first person games you can see her reflection pretty clearly in the helmet. I think other game characters often refer to her as 'she' as well (though I'm not certain of this).
