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In every game from Crystal to ORAS, the current world record (glitchless) speedrunner played as the girl. This is probably not just a coincidence. I already know that in Emerald, the Route 110 rival battle is slightly easier if you play as May and battle Brendan. Please do not question my curiosity.

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Werster addresses this question in the FAQ for most of his runs. It is generally because the male character has less dialogue.
In Heartgold and soulsilver the female rival has an animation the boy rival skips
This answer is obviously incomplete.
The catching tutorial is faster.
sumwun, if you don't mind me asking, what type of answer would you accept?
it's pretty apparent based on the comments that it's just faster, so what typ of answer format would you prefer? all the examples from each game?

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CRYSTAL: No difference. People just prefer Kris because she's the first playable female character and iconic.

RS: No difference in male vs female. Source

EMERALD: The male rival says less text than the female rival, and thus takes up less time. Also, for the Rival 2 fight, the male rival leads Slugma, and the female rival leads Wingull. In that fight you have to set up 2 X Attacks and an X Speed to take down the Grovyle, however the wingull knows growl. As you can only afford a maximum of 3 X Attacks up to this point (and normally only have 2), getting growl from the wingull can be a run killer. The slugma however only knows yawn and ember, and there is a full heal hidden just before Rival 2 as a safety against getting burned by ember. However, because the slugma knows yawn, and male Rival 3 has a Pelliper where female Rival 3 has a wingull, these fights are actually slower. It is still worth it regardless to choose the female though. Source, thanks SS

FRLG: gender doesn't matter. Source

HGSS: Lyra talks too much to Ethan. If you play as Lyra, you don't have to listen to her. Source

DPPt: The girl is slightly faster than the boy for speedrunning because Lucas has less to say than Dawn.
commented Mar 10 by J™

BW/2: Nothing noted here in terms of gender, just game versions.

XY: X is faster because you can keep the Battle Style on Set for the final Lyandre battle, but in Pokémon Y, this is not possible because Lysandre sends his Pokémon out in a different order. The time difference is quite small in comparison to version differences of other paired games.

When you pick the girl, your rival (Calem) will have a slower Meowstic at Coumarine City, meaning that your Hawlucha is more likely to outspeed it, which makes the run safer. Source

TL;DR: it's usually faster in either dialogue or battles

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