gender [jen-dur]
noun
1. A range of characteristics from masculine to feminine, with androgyny in the middle, that are used to define someone's sexual identity.
EX. One of the first questions that you're asked in all the Pokemon games, from Pokemon Crystal on, was "Are you a boy? Or are you a girl?" The game gives you the question so that you can define your character by determining their gender. The results of this choice are fairly impotent; with the obvious change of your avatar's appearance, to the gender of your rival, but nothing significant. Because this choice doesn't affect your character's physical traits in any sort of significant way, this decision has more to do with gender, that is identity, rather than sex, which is biological.
Perhaps in the future there will be more flexibility in this decision...or perhaps not. Its hard to say. But I know I'm not the only one to do a playthrough of Pokemon as a female sprite for the novelty. At least once.