I saw some theories that anime isn't about caucasians so much as Japanese just draw a "generic human face"- two big dots for eyes, cute nose and mouth. The colors come simply from trying to differentiate characters from one another. (In a country that has little facial structure difference and they all have black hair, light skin.) All the "normal" characters look like this and are assumed to be "normal" (read: Japanese.)
When they go out of their way to draw "abnormal" characters (blatantly Chinese, blatantly American, blatantly black) they go exaggerate the most obvious characteristics they can see. Which is why ironically even Japanese draw chink Asian eyes on Chinese characters, etc.
tl;dr artistic representation of human beings based on standard cultural assumption theory