Mother 3’s battle system doesn’t work on emulators. That’s because the process of emulating always introduces some amount of input lag, that is, a delay between what you see (and hear) on the screen and when the emulator is actually capturing your input
This is especially problematic in Mother 3, because when you attempt to tap the a button in the battle music rhythm system, the opportunity to hit at the right time and build up combos is very tight. A good way of thinking of it is that there is a window when the system expects you to tap the a button that corresponds to the beat of the music, and that “window” is very small. So when you play on a GBA, it can be challenging to hit the rhythm consistently. On the GBA, that’s pretty cool, because you feel rewarded when you are able to hit the rhythm and get that extra damage.
However, because the window is so tight, the input lag of emulators makes it virtually impossible to hit the rhythm in Mother 3. The only way to really hit it is to tap early, and even then it is extremely difficult.
I’m not very good at romhacking, but I have an idea of it. There must be some code in the game that does something like:
1. “start window to press A button for rhythm system”
2. “check if user has pressed A button”
-2a. “if user pressed A button, register combo hit”
3. “close window”
Wouldn’t it be possible to modify the battle code so that the system allows input for a few extra cycles? Then, Mother 3 would be fully playable on emulators. This would make it “easier”, technically, but effectively just makes it possible to use the rhythm system.
Some people might say that mother 3 is fully playable without the rhythm system working. I would respond that Mother 3 is fully playable in Japanese.