Because it deserves its own separate post, I want to address everyone who has ever compared a new Zelda game featuring an option for Link to be female to "making Samus a man."
There are several reasons this comparison doesn't stick, but first I want to say that the comparison itself strikes me as aggressive. My honest interpretation is that those who say something like this must feel threatened by the idea of Link being female, because they respond with a kind of threat of their own: "Well what if I made Samus male, how would you like that?" Samus is singled out in this case, obviously because she would be a female character being changed to a male -- like some weird example of mutually assured destruction, this should make those who support female Link think twice about the idea. The assumption being made is that anyone advocating a female Link is doing so out of a desire for greater female representation in games, even at the cost of iconic male characters, and therefore changing an iconic female character into a man is seen as a counter-point.
It is not. Link and Samus are nothing alike. Let me count the ways.
The most immediately apparent difference is that making Samus male would create the mother of all continuity errors. Samus is a person. She has 8 games and a manga detailing her entire life from her early childhood to -- what, her mid-20s? She cannot suddenly be a man after that or at any point in-between those stories. I suppose she could get a sex change within the story, but there would have to be a reason for that. Otherwise it would be total nonsense. You could also reboot the entire series with Samus as a man, which is a marginally more appealing proposition in the wake of Other M, but it is unlikely that anyone responsible for the series (or any of its fans!) would be willing to throw the baby out with the bath water that way.
You run into this same problem with Link if you try to change the gender of an established Link. In other words, if Majora's Mask starred a female Link, it wouldn't make any sense. It wouldn't jive with Ocarina of Time. This is more than an aesthetic difference: Link, as the story is told in Ocarina of Time, must be a boy. The story has to be changed significantly if you want to make Link a girl. The same is not true of any hypothetical future installment in the series, because no such story yet exists. Nothing at all -- not one thing -- in the established lore of the franchise indicates that Link must be male. A brand new hero taking up the Master Sword who happened to be female would not cause a continuity error any more than a hero with blue hair would cause such an error. Anyone familiar with legacy characters should have an easy time understanding this.
Another very important difference between Samus and Link is that Samus' gender is thematically relevant. Samus assumes the symbolic role of a mother through most of the series -- this has been with the games since long before Other M was even conceived. Since the end of Metroid II, this has been a vital part of her character. Her maternal response to the baby metroid was her main motivation for her actions in Super Metroid, probably still the most important entry. Not to say that a man cannot assume a maternal role, but this is the reason Samus' gender is important in the same way Link being a Hylian is important. Link's gender -- in general, across the series -- has no significance attached to it. Thematically, it is not necessary for Link to be male in the next Zelda game. Samus, however, is mostly defined by her relationship with the baby metroid. This was the only non-antagonistic relationship Samus displayed until the introduction of Adam Malkovitch in Metroid Fusion, and it is still the most integral to her character.
I won't abide by any more comparisons between having a daughter and getting a sex change. The two situations are not alike in any way. Bringing up Samus in this discussion is not an argument of any kind. It is a deflection of attention away from the subject at hand, a diversionary tactic used by the side of the debate who has no legitimate tools such as reason at their disposal.
