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I don't know what's included in batocera, but obviously, there's a big difference between GBA and NES/SNES multiplayer.
NES/SNES multiplayer is one system with 2 controllers plugged in. To do multiplayer on GBA each player needed their own GBA, and you'd link those together. So if you emulate that on one device it would have to emulate 2 or more systems at once.
As a handheld console, the GBA hardware was explicitly designed to support exactly one player. To play multiplayer GBA games on real hardware, either the game must have some kind of "hotseat" mode, or you need to have multiple consoles connected via link cables.
A "hotseat" game should run just fine on an emulator without any tweaking, so I'm guessing that's not what you want.
That means you're wanting to emulate multiple GBAs at once. But RetroArch is designed to run only one instance of one emulator at a time. I'm somewhat surprised to learn (although I suppose I shouldn't have been) that someone has created a RetroArch core that emulates two Gameboys/Gameboy Colors at once. But it doesn't look like anyone's done the same for the GBA. So AFAIK your only option is to have two separate Batocera devices (one for each GBA) connected over a network (if that's possible with your Pi and the emulator supports it).
Yeah but only with netplay and you need two systems or on a desktop emulator two instances of the game running.
To my knowledge, the emulator batocera uses for GBA doesn't currently support multiplayer. Only the normal GB and GBC.