I loved it and it bugged me.
As a metaphor for apartheid? It seemed to work quite well. I just can’t quite imagine something like that happening if aliens really showed up, though. If nothing else, I know personally at least one person who would sell everything he could get his hands on to buy a ticket to South Africa and live among the prawns and learn their ways. He’s not just a xenophile, he’d find these specific aliens specifically intriguing. He’d be the Jane Goodall of the prawns. I kept thinking “Eddy would give his right arm to be here.” 
I think the main human character was incredible. And I think the idea of “Christopher” being the only ‘intelligent’ one among them makes a little sense: if they really were like worker ants or bees, they could breed for genetic predisposition to castes: scientist, worker, soldier, queen, whatever. But only queens should be able to lay eggs, so children being born down here doesn’t work well for that. Still, they aren’t actually ants, so who’s to say? Anyway, I have the feeling that burning creches was probably pretty common as population control. That horrified me more than anything else, even Wikus losing his teeth and fingernails, and may I just say I think I’ve developed a new phobia?
Perhaps it went all Lord of the Flies – er, prawns – up in the ship and they’d lost a lot of their culture. Perhaps it was a generation ship… no, that doesn’t make sense, since Christopher was only three years from home.
I kept thinking: “They had no Mandela.” It seemed unreasonable to me that there was never any leader born to them. Again, I suppose it makes sense if they’re mostly uneducated semi-sentient aliens, but if that’s the case, why was Christopher so keen on rescuing them? They are his people, yes, but if they’re just a lot of workers, his species can breed more. If he’s interested in rescuing them, that might indicate the possibility of individuality among them. There are individuals worth saving.
But as a metaphor for apartheid, it seems to work fabulously.