Ok, so I've only skimmed the entire conversation, but what about birds of paradise? They're darn colourful and seem to have kept at it! The Na'vi would probably have completely different tastes in colour (haha, English) than we'd assume. Just because the norm is blue, what's to say there are no yellow groups on the other side of the world? Same goes for human colours. And just because someone's black and the other's white, well, there are plenty of couples like that, so why could it never happen to the Na'vi and multicoloured offspring occur? And if you've had a high school education and start complaining about alleles and dominant and recessive genotypes, I am 90% sure they oversimplify that stuff at school too much and have reasons for thinking that, protein snips being one of them. Besides, that thing about the skin pigment seemed viable enough, that happens here too even!
Quite frankly, those colour morph pics are awesome! My favourite is probably the red