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Yup, I sometimes like the opposite genders outfit so I would go with it, or when I have the two different versions I'll be a boy in one and a girl in the other.
I am a girl but I will play with BOTH genders. I buy both versions of the game and I almost always choose the opposite character as the one I chose the first time.
I've played as May multiple times during the days of Pokemon Emerald. The first time was kinda funny, because of the idea of me playing as the female protagonist. The other times was because I was bored and had nothing else to do.
I usually pick the girl because the boy's design just fails. The only girl's design that I don't like is May in Ruby / Sapphire. She look's like she's trippin' everywhere when she runs.
But of course, whenever I first get a new game, I always pick the boy. I usually then do another run through as the girl.
I think pretending to be a girl as a guy, or vice versa, is pretty weird. I mean these people should probably just do that in real life instead of bottling up these urges. It's healthy really.
Usually in my first few playthroughs I'll play as the character of my actual gender (female). After a while I'll do a few playthroughs as the male, just for a change of pace. It's only a sprite; doesn't mean much one way or the other.
... In SoulSilver, though, I specifically chose (and planned to choose) the male character because A) I dislike Lyra's design, and B) nostalgia. Silver Version was my first real Pokemon game; in Silver there was no female character option.
I tend to do it every now and then on some playthroughs. It can get kinda boring being forced to look at the same sprite all the time and it's a good way to add some variety.
Althought I prefer to use my own gender, I only pick the female character to see what the dialogues would look if I played as her or (in the case of Castlevania 64, for example) to see what is the difference of using the female character.
Which ever one looks better is the one I generally pick. I love Kris, but alsolike Gold, so it's 50-50 on that one. I like Brendan, and may's back sprite looks stupid. I much prefer DP Dawn to DP Lucas, but in Platinum, that's not the case, i like both, but usually choose Lucas. In HgSS I always use Ethan, cannot stand Lyra's look. I like both the BW characters.