Very good discussion. I, too, have always wondered this. Not so much the big anime eyes, because cartoon. Moreso the different colours of hair and eyes. There is no way to say this without it sounding racist (but I assure you, racism is not my intent): The vast majority of Japanese, indeed most southeast Asian people, have straight black hair and brown eyes. I've read before that Japan has one of the most homogeneous populations of any civilised country. So why do most Japanese cartoons/comics feature characters with blond, brown, red, (and blue, pink, green, purple, etc) hair, and with blue, green, grey, amber, (and very often, mismatched) eyes?
My guess is this: Cartoons are meant to be colourful. We've all heard the story that the Simpsons were given yellow skin so that they'd stand out to a channel surfer, but what of Marge's blue hair? Their bright pink house (or orange, depending on season/episode), decorated in colours no sane person would ever use? Marge's bright green appliances? Their kitchen's orange cupboards with pink/purple doors? Homer's pink 1973 Valiant?
Because cartoons are supposed to be colourful, or more accurately, they are more compelling when colourful. Cartoons are also meant to be fantasy, and fantasy also looks better when brightly coloured. Voltron's coloured lions look cool, but in real life if such a robot existed the lions would likely all be the same colour (for a more congruent assembled robot). Also, "Blue lion, Red lion", etc, sounds better than "Lion #1, Lion #2" or "Left forearm lion, Torso lion", etc.
That's just my two cents though... And they're Canadian cents. Canada doesn't even have pennies anymore, so that says something for the value of my two cents...