Nojima only worked on the original FFXIII, though. He wasn't involved in the two sequels. Kitase, on the other hand, was involved in the stories of all three games. Also, due to being the producer, he likely had final say in the scenarios. This is evident in him telling Toriyama to add Noel to FFXIII-2 despite Toriyama wanting otherwise. Watanabe just writes the scripts based on the base story he's given; he isn't really a creative mind for what the story should be, as that comes more comes from Kitase and Toriyama. For example, the base story of FFX-2 was by Kitase and Toriyama, while Watanabe just wrote the script with Nojima.
This is definitely apparent in their recent games. FFXII, produced by Ito, was Open World with barely any cutscenes, while FFXIII, produced by Kitase, was very linear with too many cutscenes. They really balance each other out.