I don’t know a whole lot about the script but from what I’ve read online it’s likely that Pinto would be playing Stewart, a female scientist who works with Franco’s character. Cheadle could be playing the human villain of the film whose mistreatment of the apes leads them to want to revolt against humans. Of course, that’s not 100% but based on some of the script beats that have been revealed, it seems to fit the actors.
Also it should be mentioned that both Cheadle and Pinto have only been offered the roles in the film and could easily turn them down. Rupert Wyatt (THE ESCAPIST) is directing the film for a June 24, 2011 release date.