If it is a game like runefactory 4 I'll choose girl then boy. Majority of the time it is a girl for me. Always seemed strange picking to be a guy to me.
Recentlly, I restarted Sapphire, and chose girl. Besides sprites and outfit, it's the same as the boy... So well, I sort of don't care too much. It was nice to see they added the girl in those games back in the day.
I just default towards the boy for no particular reason, It's not like the games have any from of indepth character customization (Even X/Y don't, really.) so I never felt the need to choose a specfic gender.
The male one. It's a role playing game, so naturally when I'm playing, I imagine I'm the character in the game trying to be Pokemon master. Since I'm a guy, it's really hard to put myself in a girl character's shoes when playing, and I find it hard to concentrate because I'm not as engaged in the game compared to when I use male characters. That's why I just stick to male Pokemon characters, even though after a while it gets boring because you can't customize their appearances (in the older games).
I don't really care who I play with, as in, when I get stuck with a male protag I don't care. But if I do have the choice between female and male I'd go female. Unless you'd actually use the female to battle with like in some MMO's, the voice acting can sometimes make me feel a bit uncomfortable, especially when my roommates point out it sounds like I'm watching porn d:
I use to choose the female characters for Pokemon, but for my moon game I decided to make the character male. I have to say, I do prefer female characters over male ones for the clothing options, (they always get better outfits and more of it too) but I'm sticking to making my avatars on games male now.
I choose the dude since I am a guy. Don't really see a point in choosing the opposite gender, it doesn't really change the story and give any bonuses. Plus I just feel more comfortable playing the male protagonist when I have the option.
I like to be a guy in this game. It does feel good to be a male character in a game. It can be different sometimes. Whenever I am getting bored then I use to be a girl to get out of that condition. It is a game so it is not difficult to be anything. LOL !
I'll always choose female for me since I'm a girl. It's really weird to choose a gender that is not yours.