As long as SM remains unrestricted, I can't really see Bee winning this fight. Bee incorporates the Hachibi into almost every aspect of his fighting style, and that's specifically why he's called the perfect host. Naruto has only just started really connecting with the Kyuubi, and hasn't had time to form that bond. Actually, he tries not to use the Kyuubi before he went for KM, and tried his best to stick to his own powers when fighting. I'm not trying to downgrade Bee, as he took on team Taka for a while and didn't resort to his transformations.
When you compare his performance to what SM Naruto has though... it just doesn't equal out. Being able to use hundreds of clones, forming huge Rasengans out of nowhere, amazing physical strength, awesome speed, versatile summons, strategic abilities, throw-able FRS... must I continue? Some may say that Samehada makes Bee almost invincible, but that really isn't true - remember that Naruto took out the Preta path w/ good backup... the one with shared vision and the other paths to help him out. Plus there's the whole Lightning < Wind and what not.