On the one hand, it's important to strike a balance of characters in any form of media. In order to seem politically correct and unbiased, you need a mix of sex, race, age, etc. in any character roster. But honestly, I hate that kind of thing. When you can tell that a character was only added to fill the female quota or something like that, it really detracts from said character.
I think you'd be safe with the entire E4+champion being male. Honestly, it's fair--the Elite 4 are just that: elite trainers. If they're the best of the best, it doesn't matter what their gender is. It just means they overcame all challenges and have proven themselves to be better trainers than everyone else. To add an arbitrary female to the group--just for the sake of having a woman in there--would detract from the purpose of having an Elite 4, imo.
But since you're just making a game and not the actual Pokemon League hiring trainers, that second argument doesn't really hold as much water. :P You should technically be going for a balanced cast but if you're only adding a female for the sake of adding a female, I wouldn't bother.