Man, there are so many ways this could go! I don't think they'll stick so much with the apartheid theme in the second one, and focus more on the Prawn integration with humanity.
My personal theory is this. Christopher Johnson was one of the Prawn's leader caste. That's why he was able to manipulate their technology efficiently, and was far more intelligent than the other Prawns.
Wikus now being a Prawn, with evidence of higher intelligence, like Christopher, is trying to lead a resistance effort against the guards at District 10. As part of the leadership caste, Wikus is able to rally a group of Prawn rebels who escape District 10, and set up a refugee base in the wilderness of South Africa. From there, they wage a guerrilla war against MNU, holding out until Christopher returns to rescue his people, and return Wikus to his original form.
Themes could involve revolution, integration, and interspecies relationships, the last one regarding Wikus and his estranged wife.
But then, thats just my theory