I dont think Naruto should ever learn to control the actual Kyuubi. It's what makes the Kyuubi so terrifying, because it can't be tamed and it won't share it's power with its host. (When I talk about it sharing it's power I'm referring to what the 8tails told Naruto when KillerBee was training him). The ability Naruto has now to control the Kyuubi's chakra is enough I think and it makes him strong as he needs to be.
If anything, I think it's something for when he has to fight Sasuke. A genjutsu counter would be my guess because that's what Sasuke has that can completely destroy Naruto and Itachi knew Naruto was weak against genjutsu. Itachi also intended to help Sasuke gain his Mangekyou Sharingan because he went to fight Sasuke afterwards so it was even more reason for him to help Naruto to counter Sasuke's Sharingan.
Itachi also said that he hopes the day never comes when Naruto has to use it. He could have been referring to the day Sasuke decides to destroy Konoha or just fight against Naruto in general.
