According to New York Magazine’s Vulture — Entertainment & Culture Blog, producer Goetzman says that Jonze will have the final cut and that:
… reports about Warner Bros. being unhappy with the performance of Max Records, the film’s young star, as well as rumors about pants-shitting children at test-screenings, are 100 percent untrue (though we’re pretty sure he couldn’t possibly have confirmed these even if they were true), and he implies the film’s problems have more to do with practical issues stemming from Jonze’s aversion to CGI. “Spike wanted to do things low tech,” he told CHUD. “He wanted big animatronic Wild Things in the jungle, which look great. As you go deeper in the jungle and weather sets in … We misjudged that, production-wise.” The good news is, though, that Goetzman claims Jonze will have final cut on the film. So, when it’s released sometime next century, you can rest assured it will be his original vision, provided Jonze lives that long.