IMHO, the difference between ball and pear is for the WAY you grip it. In most games where you're concerned with directing your character in a particular direction, like up, down, left right, Ball is ideal, and you would grip it fully on top.
Whereas, the pear shaped I think made its appearance with Street Fighter 2, and is better suited for making "rotation" movements etc (for the special moves), and you would grip it almost like a trigger stick.
only my opinion though...