Big eyes represent innocence. It's why a show like Psycho-Pass has characters with all normal sized eyes and one character, a new inspector fresh out of training, has eyes 3-4x bigger then theirs.

The eyes are oversized because otherwise facial expressions (and the ability to tell which character you're looking at) become quite difficult to express. That's the reasoning behind the exaggerated expressions and stuff too. Met a guy once who draws this stuff, and he talked about it a bit.

Ever watched American cartoons? Why does everyone look retarded?