I'm fine having to play a female character, why should not having your specific gender as the player character matter?
Because it's important to those people to have their gender represented, and it's important to them because Pokemon is important to them and thus they want their beloved games to be able to reflect who they are.
I mean, in X and Y you could choose your character to be darker-skinned. That was a huge step for Nintendo.
I think that having a single, gender-neutral character will help Nintendo, actually. You could get a boy's or girl's haircut and clothing if that's included in the next game.
The games also address you as gender-neutral (never once does the text say she/hers) so text isn't an issue either.