To the OP: Practice is all you can really do. The time between sound, controls, and graphics is slightly off if you don't play it on an actual cartridge or on a PSP.

In Mother 3 When a character uses their basic attack command, pressing the A button or L button in time with the beat of the music will allow them to achieve extra hits, which are each weaker than the initial hit. Put enemies to sleep to listen to the beat and go from there. It's not impossible to overcome, but keep it in … A lot of songs don't have steady 1-2-3-4-1-2-3-4 beats (in fact, I'd go so far as to say that the songs with steady beats are in the minority), so that could be what's messing you up.