PRELIMINARY RESULTS: after consulting with our finest scientists, we have come to the conclusion is that what's likely going on is how many frames it takes to access the flash differs, which alters how far in the (buggy, nonrandom) random stream Emerald is when it attempts to randomize the gender. Hence, for a given cartridge/console combo or given emulator, it will tend to be either all boys or all girls. (Sounds like all boys is more common.)
INCREDIBLY SPECIFIC REQUEST: do you have a real, normal Pokemon Emerald cartridge and a way to boot it? Please power it on, wait several seconds for the player character to appear on a bike, and note their gender. Power the device off and back on and do this several times, at least 5. Please tell me: how many boys, how many girls, what language your cartridge is in, and what platform you booted it on (original gameboy advance, gba sp, nintendo ds, whatever)
I am asking this because I am observing the behavior in emulator that Ruby/Sapphire correctly randomize the player gender but Emerald always picks girl (which is what I expected because its rng seeding is buggy). However, there are recordings of the Emerald opening on youtube that show a boy. Presumably this is caused by emulator differences, but I really want to know which reflects the game on real hardware.
Another edit for clarity: Emerald's RNG is buggy specifically because they forgot to seed the RNG from the RTC time. Ruby/Sapphire do not forget. If you have a R/S cartridge with a working clock, it should be random, as it is in emulator. If it is dead, it will have the same issues as Emerald
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