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Previously it was mostly dependent on if it was my main play-through of a game or the secondary run (like nuzlockes or whatever). So in my main I'd use the boy, but in the others I'd use the girl. It also depended on how much I liked the models:
Crystal I'd go with either of them
FR/LG I'd always use Leaf because she's my favorite
Emerald either
DPP either
HG/SS was previously just Ethan (I've grown to appreciate Lyra)
B/W is Hilbert (I've only JUST started liking Hilda, so if I ever play it again I might go with her)
B2/W2 Rosa
Then there's the games with customization. With XY I'd go with either of them since there's some good stuff on both sides, but with SM/USUM it's purely Chicken since Sun has shit all in regards to customization. If customization remains a thing I'll probably keep picking female, but if they add crossdressing or just add more suits and shit then I'd likely use the male characters more.
So the sum up, I go with either PC for the most part, but I like some of the females better than the males so I play as them.