I think you're right about the input registering system that it might need to be a bit more patient. For instance, instead of executing a 'walk' command immediately right after the input, the game could wait for, say, 5 frames then decide to 'walk' or to 'attack', etc.
I have theory that the game wouldn't let you do a regular attack or attack in charge mode because you ran out of MP which I think I could add something to alert the player about that.