Almost all GBA metroid runners prefer to play on their GBA SP; when playing on a GC with a GBA player, we use a GBA SP as the controller with the GBA-GC link cable.
Dragonfangs is probably the main runner who runs primarily on VBA-RR (i think), which emulator is generally fine because we go by in-game time.
You can always try to use a GC controller but uh... the tiny d-pad <_< Or you can pull a dragondarch and use the stick