Gender makeup and dynamic in a work of fiction is an interesting topic. The reason Azumanga Daioh works, for example, is that its cast almost entirely consists of women and girls. If one of the girls was a boy, it would have just turned into yet another harem. Even if there was nothing of the sort in the text, people would still have read that into it, and been distracted from the more interesting dynamics between all of the characters.
Similarly one of the factors that makes Cowboy Bebop stand out is the presence of a gender non-conforming character in the main cast. Is Edward a girl, a boy, or somewhere in between? It doesn't actually matter. Edward is referred to as a girl and doesn't seem to object to it, but chooses to go by a traditionally masculine name and presents very androgynously. As a result, rather than us seeing Ed's world as the world of a young boy or girl, we simply see it for what it is. Cowboy Bebop's world through the eyes of an innocent. A volatile genius innocent, but an innocent nonetheless. Our preconceptions are thrown out the window and we are left with a far better view of a far more interesting character as a result.
There's also the matter of how femininity and masculinity are explored in a work. In most cases the gender of characters play little influence, but in some it's all important. FLCL would be completely nonsensical if Naota was a girl, because FLCL is all about what it's like to be a boy going through that transition between childhood and adolescence.
